title: 30min_mock_rep4

value: 30 min


title: m_228

status: Public on Nov 22 2019

type: SRA

city: Gainesville

first: Rhonda

last: Bacher

state: FL

address: 2004 Mowry Rd.

country: USA

institute: University of Florida

description:
mm10genes.no_mt.ec.tab
mm10genes.no_mt.tpm.rescale.tab

library_source: transcriptomic

data_processing:
Illumina bclToFastq-1.8.4 used for basecalling the HiSeq2500 Files, and bcl2fastq2-v2.17.1.14 for basecalling the HiSeq3000 Files.
Reads were filtered and trimmed for adapters and quality. Expression estimates were calculated using RSEM v1.2.3 with alignments by bowtie v0.12.9 to mm10 (mouse) & hg19 (human) transcriptomes.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg19 & mm10
Supplementary_files_format_and_content: Tab-delimited text files include expected count (EC) values and TPM-normalized counts for each sample.

molecule: total RNA

organism: Mus musculus

growth_protocol: H1 human ES cells were routinely maintained as undifferentiated in E8 medium. Mouse Epiblast stem cells (mEpiSCs) were maintained on MEFs in TSS maintenance medium (DMEM/F12 (Thermo Fisher Scientific, USA), 20% knockout serum replacement (Thermo Fisher Scientific, USA), 0.18 mM B-mercaptoethanol (Sigma, USA), 1 X non-essential amino acids (Thermo Fisher Scientific, USA), 2 mM L-glutamine (Sigma, USA), 7.5 ng/mL activin A (R&D Systems, USA), and 5 ng/mL bFGF (R&D Systems, USA))

extract_protocol:
Cells grown in 6-well or 12-well plates were washed with PBS and lysed with RLT Plus lysis buffer (Qiagen), stored in -20C for 24 hours and then -80C until later processing. Total RNA was purified from the RLT Plus lysates using the RNeasy Plus Mini Kits (Qiagen) according to manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard the LM-seq protocol.

treatment_protocol: Neural differentiaion was induced with neural induction medium (DF3S (Thermo Fisher Scientific, USA) supplemented with 1 X N2 supplement (Thermo Fisher Scientific, USA), 1 X B27 supplement (Thermo Fisher Scientific, USA), and 100 ng/µL of mNoggin (R&D Systems, USA)). Control medium consisted of E8 pluripotency maintenance medium for H1 cells.

tag: cell line

tag: cell type

value: Mouse Epiblast stem cells

tag: treatment

value: Neural induction medium

tag: time

value: 228 min


title: m_188

value: 188 min


title: m_176

value: 176 min


title: 30min_mock_rep2

city: Mohali

first: Hasthi

last: Ram

address: Sector 81

department: Agriculture biotechnology

country: India

institute: NABI (National Agri-Food Biotechnology Institute)

data_processing:
The first phase of the data analysis pipeline was the quality control step. In this step, the quality of the raw sequencing data was assessed using the tool FastQC
Bases with bad quality (Phred score <20), over-represented PCR primers and bases with fluctuating GC content identified in this step were pruned using a combination of Cutadapt and Seqtk  tools.
The second phase of quality control was the removal of rRNA reads from raw sequencing data.
For aligning the filtered raw data, we used the standard Arabidopsis genome annotation, TAIR10, and used TopHat tool.
we used the python package HTSeq to count the reads that are aligned to each genomic feature (exon) and to generate gene expression read count matrices. For identifying the deferentially expressed genes from the read count data, we used the R package DESeq2, which models read count data following a negative binomial distribution
Genome_build: Arabidopsis genome annotation, TAIR10
Supplementary_files_format_and_content: .csv file having gene ID and number of counts in tab delimited format

organism: Arabidopsis thaliana

source_name: shoot apical meristem

growth_protocol: Plants were grown on soil in short day conditions for 4-5 weeks before harvesting

extract_protocol:
Rneasy Mini kit (Qiagen) was used according to manufacturer’s instruction for RNA preparation
RNA-Seq Libraries for all the samples were prepared using ‘TruSeq Stranded mRNA Library Prep Kit from Illumina'.

treatment_protocol: Plants were treated with 1 mm IAA+lanolin paste or mcok paste for different time points. About 10 SAM  were quickly harvested and qucik forzen in liquid nitrogen for one biological replicate.

value: mock paste

tag: time point


title: m_172

value: 172 min


title: m_168

value: 168 min


title: 30min_mock_rep1


title: 12hr_IAA_rep1

value: IAA paste


title: m_160

value: 160 min


title: m_164

value: 164 min


title: 30min_IAA_rep3


title: m_156

value: 156 min


title: m_152

value: 152 min


title: m_148

value: 148 min


title: m_140

value: 140 min


title: mip130 RNA rep2

city: Cardiff

first: Helen

last: White-Cooper

address: Museum Avenue

country: United Kingdom

institute: Cardiff University

data_processing:
Base calling was performed using the Phred algorithm, limiting base calls to a Q-score of ≥30
DNA sequence alignment was performed against the dm5.53 genome release and annotation (dos Santos et al. 2015) using Bowtie v1.1.1 with parameters -v 3  --trim3 14 --maxins 5000 --fr -k 1 -p 15 --sam
The .sam file was separated into chromosome specific files using the bash script chrgrep.sh (see supplementary files for all scripts)
The chromosome specific .sam files were processed using SAMparser.plx to extract DNA fragments of a user defined insert length range (or ISIZE). The output .txt files for replicates were pooled using the UNIX "cat" function.
The .sgr files were processed with histogram.plx, which calculated dyad frequency for individual 10bp bins across each chromosome. A 3 bin moving average is applied by histogram.pl for light smoothing of the data, which was output in .sgr format.
Scaler.plx was used on the .sgr output for the X chromosome using a scale factor of 1.5 to account for the detected copy number variations found in the S2R+ samples.
Dros_cat.sh was used to pool all of the chromosome specific files into a single genomic .sgr
RNA sequence alignment was performed against the dm5.53 genome release and annotation (dos Santos et al. 2015) using Tophat v2.0.12 with parameters -i 40 -p 8 -o  -G --library-type fr-secondstrand
Quantification of mapped reads was performed by Cufflinks with parameters -o –u –b  –g  –p 8 --min-intron-length 40
Assemblies were merged using Cuffmerege with parameters -o -g –p 8 -s
Normalization of read abundance values across samples was performed using Cuffnorm, with parameters -o -L -p 8
Genome_build: dm5.53 (dos Santos et al. 2015)
Supplementary_files_format_and_content: .bedgraph files: generated from the genomic .sgr containing number of fragments of a particular size range (+/- 0.2 for 150 and 225 fragments, +/- 10bp for 110bp fragments) with dyads mapping to the bin.
Supplementary_files_format_and_content: FPKM_expression_table.xlsx: Excel spreadsheet containing FPKM values for each transcript across each sample.

organism: Drosophila melanogaster

growth_protocol: Approximately 5x106 S2R+ cells were plated on 25cm flasks in Shields and Sang insect media with 10% heat-inactivated fetal bovine serum (FBS). All samples were passaged an identical number of times before use, and all were incubated at 25oC throughout growth and treatments.

extract_protocol:
Chromatin (DNA) preparation: Cells were washed twice with 1X PBS, then gently permeabilized using 950µl spheroplast digestion buffer containing NP-40 (SDBN, 1M Sorbitol, 50mM NaCl, 10 mM Tris-HCL [pH7.5], 5mM MgCl2, 1mM CaCl2, 0.5mM Spermidine, 1mM β-Mercaptoethanol, 0.075% NP-40). Micrococcal Nuclease was added to a final concentration of 600U/ml, and the plate was gently rocked for 3 minutes at room temperature. The reaction was stopped with 100µl STOP solution (5% SDS, 250mM EDTA). DNA was extracted using 2 phenol/chloroform purifications, with RNase treatment (5µl, 10mg/ml, 30 minutes, 37oC) after the first purification. 100% ethanol containing 0.3M NaOAc was used to precipitate DNA.
RNA: Cells were harvested from 1x4cm area of plate after PBS washes (see chromatin protocol) but before digestion. Total RNA was harvested using the RNAeasy mini kit (Qiagen) as per manufacturer's guidelines.
NKD DNA: The genomic DNA extracted from a single fly was incubated with 22u/ml Mnase for 20 seconds.  The reaction was stopped with 100µl STOP solution (5% SDS, 250mM EDTA).  RNase treatment (5µl, 10mg/ml, 30 minutes, 37oC) was followed with DNA extraction using a phenol/chloroform purification. 100% ethanol containing 0.3M NaOAc was used to precipitate DNA.
DNA: All sequencing performed by Exeter University Sequencing service. Standard Illumina protocols were performed for samples being sequenced on a Illumina HiSeq 2000 machine running in paired-end 100bp mode. During size selection, primer dimers were removed and all other DNAs were used for sequencing.
RNA: All sequencing performed by Exeter University Sequencing service. Standard Illumina protocols were performed for samples being sequenced on a Illumina HiSeq 2000 machine running in paired-end 100bp mode. RNA was run through an oligo dT column prior to cDNA generation to filter for mRNA transcripts only

treatment_protocol: RNAi treatments were carried out over 4 days, with cell harvesting on the end of the 4th day. At the start of each day, the media was aspirated from the sample and 30µg/ml of the desired dsRNA in FBS-free Sheilds & Sang insect media. This was followed by incubation at 25oC for 30 minutes, after which S&S insect media with 10% heat-inactivated FBS was added to achieve a final dsRNA concentration of 10µg/ml.

tag: agent


title: m_144

value: 144 min


title: NKD DNA

library_source: genomic

molecule: genomic DNA

source_name: Drosophila melanogaster


title: 30min_mock_rep3

value: 30 min


title: m_136

value: Mouse Epiblast stem cells

value: 136 min


title: mip120 RNA rep2


title: mip120 RNA rep1


title: mip130 RNA rep1


title: m_120

value: Neural induction medium

value: 120 min


title: mip40 RNA rep1


title: GFP RNA rep2

value: GFP


title: m_128

value: 128 min


title: mip40 RNA rep2


title: m_116

value: 116 min


title: 30min_IAA_rep1


title: 30min_IAA_rep2


title: m_124

value: 124 min


title: GFP RNA rep1


title: m_108

value: 108 min


title: mip130 DNA rep1

description:
mip130_150bp.bedGraph
mip130_110bp.bedGraph
mip130_225bp.bedGraph


title: mip120 DNA rep2

description:
mip120_150bp.bedGraph
mip120_110bp.bedGraph
mip120_225bp.bedGraph


title: m_100

value: 100 min


title: m_112

value: 112 min


title: E2F2 RNA rep1


title: mip120 DNA rep1


title: m_92

value: 92 min


title: m_96

value: 96 min


title: E2F2 DNA rep1

description:
E2F2_150bp.bedGraph
E2F2_110bp.bedGraph
E2F2_225bp.bedGraph


title: mip40 DNA rep1

description:
mip40_150bp.bedGraph
mip40_110bp.bedGraph
mip40_225bp.bedGraph


title: GFP DNA rep2

description:
GFP_150bp.bedGraph
GFP_110bp.bedGraph
GFP_225bp.bedGraph


title: mip40 DNA rep2


title: GFP DNA rep1


title: m_80

value: 80 min


title: m_76

value: 76 min


title: m_72

value: 72 min


title: m_84

value: 84 min


title: m_64

value: Mouse Epiblast stem cells

value: 64 min


title: mip130 DNA rep2


title: m_56

value: Neural induction medium

value: 56 min


title: m_104

value: 104 min


title: m_68

value: 68 min


title: m_52

value: 52 min


title: m_48

value: 48 min


title: m_44

value: 44 min


title: m_88

value: 88 min


title: SA89

type: protein

city: Guangzhou

first: Huihua

last: Zhang

address: 601, west Huangpu avenue, Tianhe district

department: Biomedicine Institute & Cell Biology Department

country: China

institute: Jinan University

description:
Sample name: 89
Secreted proteins

hyb_protocol: 5-fold diluted culture supernatant was added to each well. After overnight incubation at 4°C and extensive washing, the biotin-labeled detection antibody was added for 2 hours and then washed away. AlexaFluor 555-conjugated streptavidin was then added and incubated for 1 hour at room temperature.

scan_protocol: The signals (532 nm excitation, 635 nm emission) were scanned and extracted using an InnoScan 310 scanner (Innopsys, Carbonne, France).

data_processing: Individual array spots were background subtracted locally by subtracting the median background across spot replicated in each sample, and then normalized using two positive controls.

label: AlexaFluor 555

molecule: protein

organism: Homo sapiens

source_name: serum

label_protocol: AlexaFluor 555-conjugated streptavidin

extract_protocol: 5-fold diluted culture supernatant from whole blood

treatment_protocol: Whole blood was collected in vacutainer serum tubes, incubated undisturbed at room temperature for 30 min, then centrifuged at 2000 rpm for 15 min at 4 °C. The supernatant was collected and frozen at -80 °C for storage.

tag: tissue

value: serum

tag: cohort

value: first

tag: condition

value: S7 (Dampness constitution before)


title: SA84

description:
Sample name: 84
Secreted proteins

value: S5 (Balanced constitution after)


title: SA86

description:
Sample name: 86
Secreted proteins

value: S6 (Balanced constitution after)


title: SA85

description:
Sample name: 85
Secreted proteins

value: S5 (Dampness constitution before)


title: SA87

description:
Sample name: 87
Secreted proteins

value: S6 (Dampness constitution before)


title: m_424

value: Mouse Epiblast stem cells

value: 424 min


title: m_40

value: Neural induction medium

value: 40 min


title: m_28

value: 28 min


title: m_36

value: 36 min


title: m_16

value: 16 min


title: m_20

value: 20 min


title: m_32

value: 32 min


title: m_24

value: 24 min


title: SA88

description:
Sample name: 88
Secreted proteins

value: serum

value: S7 (Balanced constitution after)


title: m_12

value: 12 min


title: m_4

value: 4 min


title: m_8

value: 8 min


title: SA77

description:
Sample name: 77
Secreted proteins

value: first

value: S1 (Dampness constitution after)


title: SA78

description:
Sample name: 78
Secreted proteins

value: S2 (Balanced constitution before)


title: SA83

description:
Sample name: 83
Secreted proteins

value: S4 (Dampness constitution after)


title: SA79

description:
Sample name: 79
Secreted proteins

value: S2 (Dampness constitution after)


title: SA80

description:
Sample name: 80
Secreted proteins

value: S3 (Balanced constitution before)


title: SA76

description:
Sample name: 76
Secreted proteins

value: S1 (Balanced constitution before)


title: SA81

description:
Sample name: 81
Secreted proteins

value: S3 (Dampness constitution after)


title: SA82

description:
Sample name: 82
Secreted proteins

value: S4 (Balanced constitution before)


title: SA74

description:
Sample name: 74
Secreted proteins

value: second

value: Dampness constitution


title: SA75

description:
Sample name: 75
Secreted proteins


title: SA73

description:
Sample name: 73
Secreted proteins


title: SA72

description:
Sample name: 72
Secreted proteins


title: ES_SOM3

city: Prague 4

first: Josef

last: Pasulka

address: Vídeňská 1083

country: Czech Republic

institute: Institute of Molecular Genetics of the ASCR, v. v. i.

description: Single-end, non-stranded

data_processing:
All RNA-seq datasets were mapped using STAR 2.5.3a
Mapped reads were counted using program featureCounts
The GENCODE gene set (GENCODE M15) was used for the annotation
See the methods for more details
Genome_build: mm10
Supplementary_files_format_and_content: CSV file containing gene counts generated by “featureCounts” program

source_name: GV oocyte

extract_protocol:
NGS libraries were generated using V2 version of Ovation RNA-seq kit from Nugen. Libraries were prepared according to manufacturer’s protocol. cDNA fragmentation was performed on Bioruptor sonication device (Diagenode) as follows: 45 s ON, 30 s OFF for 21 cycles on low intensity, 100 ng fragmented cDNA was used for further library preparation. Libraries were amplified by 9 cycles of PCR. Libraries were quantified by Qubit HS DNA kit, quality was assessed on 2100 Bioanalyzer HS DNA chip.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

tag: genotype

value: Dicer-SOM/SOM

value: GV oocyte

tag: age (weeks)


title: SA71

description:
Sample name: 71
Secreted proteins

value: serum


title: ES_SOM2

description: Single-end, non-stranded


title: ES_MTKO4

description: Single-end, non-stranded

value: Dicer-{delta}MT/{delta}MT


title: ES_MTKO3

description: Single-end, non-stranded


title: SA70

description:
Sample name: 70
Secreted proteins


title: ES_MTKO2

description: Single-end, non-stranded


title: ES_MTKO1

description: Single-end, non-stranded


title: SA69

description:
Sample name: 69
Secreted proteins


title: ES_HET

description: Single-end, non-stranded

value: Dicer-{delta}MT/WT


title: ES_WT3

description: Single-end, non-stranded

value: Dicer-WT/WT


title: ES_WT1

description: Single-end, non-stranded


title: SA65

description:
Sample name: 65
Secreted proteins


title: SA66

description:
Sample name: 66
Secreted proteins


title: SA64

description:
Sample name: 64
Secreted proteins


title: ES_SOM1

description: Single-end, non-stranded


title: SA58

description:
Sample name: 58
Secreted proteins


title: SA59

description:
Sample name: 59
Secreted proteins


title: SA61

description:
Sample name: 61
Secreted proteins


title: wt_mef_2

city: Cambridge

first: Abbie

last: Groff

state: MA

address: 7 Divinity Ave

department: Stem Cell and Regenerative Biology;

institute: Harvard University

description: All mice used for the study are Tug1_tm1.1Vlcg mice (wild types contain 2 normal Tug1 alleles (no LacZ) and homozygous knockout have a lacZ reporter in place of Tug1 on both alleles.)

data_processing:
Casava 1.8.2 was used to call bases
Reads were aligned to mm10 using tophat2 (--no-coverage-search --max-multihits 10 -p 8)
Bams were quantified using cuffquant and a modified verson of the GENCODE M2 transcriptome (--no-update-check -p 8)
Differential analysis was performed using cuffdiff2 (-p 8)
Genome_build: mm10
Supplementary_files_format_and_content: text file with cuffdiff output

molecule: polyA RNA

extract_protocol:
Tissues were harvested immediately after euthanasia, snap frozen in liquid nitrogen and stored at -80˚C. Tissues were subsequently pulverized in liquid nitrogen and homogenized in TRIzol. Embryonic Mouse Fibroblasts (MEF, passage 2) were cultured in 10cm dishes in normal conditions (37˚C, 5% CO2) and homogenized directly in Trizol.
Standard illumina protocols were used to make libraries (TruSeq RNA Sample Preparation Kit v2)

value: embryonic fibroblasts

tag: lncrna previous name

tag: background

value: C57BL/6J (N3-C57BL/6J, no Neo)

tag: official strain name

value: wt

tag: Sex

value: M


title: ko_mef_0

value: ko


title: SA68

description:
Sample name: 68
Secreted proteins


title: ko_mef_1


title: wt_mef_1


title: ko_mef_2


title: SA67

description:
Sample name: 67
Secreted proteins


title: SA57

description:
Sample name: 57
Secreted proteins


title: SA56

description:
Sample name: 56
Secreted proteins


title: SA55

description:
Sample name: 55
Secreted proteins


title: ES_WT2

description: Single-end, non-stranded


title: SA52

description:
Sample name: 52
Secreted proteins


title: SA63

description:
Sample name: 63
Secreted proteins


title: SA53

description:
Sample name: 53
Secreted proteins


title: SA60

description:
Sample name: 60
Secreted proteins


title: SA54

description:
Sample name: 54
Secreted proteins


title: SA62

description:
Sample name: 62
Secreted proteins


title: SA49

description:
Sample name: 49
Secreted proteins


title: SA51

description:
Sample name: 51
Secreted proteins


title: SA50

description:
Sample name: 50
Secreted proteins


title: wt_mef_0


title: SA48

description:
Sample name: 48
Secreted proteins


title: SA47

description:
Sample name: 47
Secreted proteins


title: SA46

description:
Sample name: 46
Secreted proteins


title: SA45

description:
Sample name: 45
Secreted proteins


title: SA44

description:
Sample name: 44
Secreted proteins


title: SA42

description:
Sample name: 42
Secreted proteins


title: SA43

description:
Sample name: 43
Secreted proteins


title: SA39

description:
Sample name: 39
Secreted proteins


title: SA41

description:
Sample name: 41
Secreted proteins


title: DRG_DMM_16wk_rep2

type: RNA

city: Chicago

first: Rachel

middle: E

last: Miller

address: 1735 W Harrison St

institute: Rush University Medical Center

description: gene expression data from dorsal root ganglion tissue collected at different times in an osteoarthritis mouse model (DMM)

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: standard Affymetrix protocol

label: biotin

source_name: DRG DMM+16wk

label_protocol: standard Affymetrix protocol

extract_protocol: none provided by the submitter

treatment_protocol: Mice were either untreated (naïve), or subjected to sham or destabilizatio of the medial meniscus (DMM) surgery in the right knee at 10 weeks of age. Mice were sacrificed 4, 8, or 16 weeks after surgery (or at age 14, 18, or 26 weeks of age in the case of naive).

tag: gender

value: male

value: dorsal root ganglion (L3-L5)


title: DRG_DMM_16wk_rep3


title: SA40

description:
Sample name: 40
Secreted proteins


title: DRG_naive_16wk_rep2

source_name: DRG naïve+16wk


title: DRG_sham_16wk_rep2

source_name: DRG sham+16wk


title: DRG_DMM_8wk_rep2

source_name: DRG DMM+8wk


title: DRG_sham_16wk_rep1


title: DRG_naive_16wk_rep1


title: DRG_DMM_16wk_rep1


title: DRG_naive_16wk_rep3


title: SA38

description:
Sample name: 38
Secreted proteins


title: SA37

description:
Sample name: 37
Secreted proteins

value: Balanced constitution


title: DRG_sham_16wk_rep3


title: SA36

description:
Sample name: 36
Secreted proteins


title: SA35

description:
Sample name: 35
Secreted proteins


title: DRG_DMM_8wk_rep3


title: SA33

description:
Sample name: 33
Secreted proteins


title: SA34

description:
Sample name: 34
Secreted proteins


title: DRG_naive_8wk_rep3

source_name: DRG naïve+8wk


title: SA32

description:
Sample name: 32
Secreted proteins


title: SA31

description:
Sample name: 31
Secreted proteins


title: DRG_naive_8wk_rep1


title: SA30

description:
Sample name: 30
Secreted proteins


title: DRG_DMM_4wk_rep3

source_name: DRG DMM+4wk


title: DRG_DMM_4wk_rep2


title: DRG_sham_4wk_rep3

source_name: DRG sham+4wk


title: DRG_sham_4wk_rep2


title: DRG_sham_8wk_rep1

source_name: DRG sham+8wk


title: DRG_DMM_8wk_rep1


title: DRG_naive_4wk_rep3

source_name: DRG naïve +4wk


title: DRG_sham_4wk_rep1


title: DRG_naive_4wk_rep2


title: SA29

description:
Sample name: 29
Secreted proteins


title: SA27

description:
Sample name: 27
Secreted proteins


title: MPs_24h_biologicalreplicate3_duplicate2

city: Maastricht

first: Héloïse

last: Proquin

address: Universiteitssingel 50

country: Netherlands

institute: Maastricht University

hyb_protocol: Hybridization was performed according to the manufacturer’s protocol on SurePrint G3 mouse Gene exp 60kv2 microarrays slides

scan_protocol: After hybridization, the microarray slides were scanned using an Agilent DNA Microarray Scanner with Surescan High-resolution Technology (Agilent Technologies, The Netherlands) with scanner settings to Dye Channel: G, Profile: AgilentG3_GX_1Color, Scan region: Agilent HD (61 x 21.3 mm), Scan resolution 3 µm, Tiff file dynamic range: 20 bit, Red PMT gain: 100%, Green PMT gain: 100%.

data_processing: First the quality of the microarrays was checked by the quality control pipeline provided by Agilent (Feature extraction software (FES) version 10.7.3.1). All samples met the quality criteria of the FES. In order to have a thorough quality check and normalize the data, an in-house QC pipeline was developed and is publically available (github.com/BiGCAT-UM/arrayQC_Module). All samples met the in-house quality check. Raw data with expression values and genes were selected for data analysis based on flags and missing values. Height groups were defined: E171 2 days, 7 days, 14 days, 21 days for the exposed samples and control 2 days, 7 days, 14 days, 21 days for the controls. Within each group, at least four out of six or five out of seven samples had to have a pass for the spot. Also, within each group, unique identifiers passed when there were less than three missing values out of six or seven values. The unique identifiers with an average expression less than four in all of the groups were omitted. The missing values were pre-processed using the GenePattern ImputeMissingValues.KNN module v13, with standard settings. Unique identifiers were removed and identical Agilent probe identifiers were merged with Babelomics 5, using the median method for pre-processing data. Next, the data was re-annotated from Agilent probe identifiers to EntrezGene identifiers (EntrezGene IDs); see Annotation_file.txt linked on the Series record.  The expression data for all genes with an identical EntrezGeneIDs were subsequently merged with Babelomics 5, using the median method for pre-processing data. Using an R-script, a Linear Mixed Model Analysis for Microarrays (LIMMA) (version 1.0) was performed to extract differentially expressed genes (DEG). The data of each control time point (control) was subtracted from the time-matched exposed mice to E171. The standard cut-off values of a fold-change (FC) of 1.5 and a p-value of 0.05 were used in LIMMA. The DEG for each time point were subsequently used in Consensus Pathway Database (CPDB) for an over-expression gene set analysis. All the available databases from CPDB were used (release 31, 1 sept. 2015) with a p<0.01.

source_name: Caco-2 cells

label_protocol: Total RNA was synthesized into cRNA and labelled according to the One-Color Microarray-Based Gene Expression Analysis protocol version 6.6

growth_protocol: cultured in an incubator under standard cell culture conditions (37°C, 5% CO2) in Dulbecco’s Modified Eagles Medium (DMEM) (Sigma-Aldrich, the Netherlands). DMEM was supplemented with 10% FBS, 1% non-essential amino acids, 1% sodium pyruvate and 1% penicillin/streptomycin. Cells were passaged at 80 to 90% confluency.

extract_protocol: Isolation of RNA was performed using the miRNeasy Mini Kit (Qiagen, The Netherlands) including a DNase treatment, according to the manufacturer’s protocols for “Animal Cells and Animal Tissues”

treatment_protocol: Controls, E171, TiO2 NPs, TiO2 MPs

tag: cell line

value: MPs


title: SA28

description:
Sample name: 28
Secreted proteins

value: second


title: SA24

description:
Sample name: 24
Secreted proteins


title: SA23

description:
Sample name: 23
Secreted proteins


title: SA25

description:
Sample name: 25
Secreted proteins


title: SA21

description:
Sample name: 21
Secreted proteins


title: SA22

description:
Sample name: 22
Secreted proteins


title: SA26

description:
Sample name: 26
Secreted proteins


title: DRG_DMM_4wk_rep1


title: Control_E171_24h_biologicalreplicate3_duplicate1


title: SA19

description:
Sample name: 19
Secreted proteins


title: Control_E171_0h_biologicalreplicate3_duplicate2


title: SA17

description:
Sample name: 17
Secreted proteins


title: Control_MPs_24h_biologicalreplicate2_duplicate1


title: SA16

description:
Sample name: 16
Secreted proteins


title: Control_E171_24h_biologicalreplicate2_duplicate1


title: Control_E171_24h_biologicalreplicate1_duplicate1


title: Control_MPs_24h_biologicalreplicate1_duplicate2


title: SA18

description:
Sample name: 18
Secreted proteins


title: SA15

description:
Sample name: 15
Secreted proteins


title: SA13

description:
Sample name: 13
Secreted proteins


title: SA14

description:
Sample name: 14
Secreted proteins


title: MPs_24h_biologicalreplicate1_duplicate1_2


title: SA12

description:
Sample name: 12
Secreted proteins


title: SA11

description:
Sample name: 11
Secreted proteins


title: Control_E171_0h_biologicalreplicate3_duplicate1_2


title: Control_MPs_0h_biologicalreplicate3_duplicate2


title: Control_E171_0h_biologicalreplicate2_duplicate1_2


title: SA10

description:
Sample name: 10
Secreted proteins


title: MPs_24h_biologicalreplicate1_duplicate1


title: Control_MPs_0h_biologicalreplicate3_duplicate1


title: SA9

description:
Sample name: 9
Secreted proteins


title: Control_E171_24h_biologicalreplicate2_duplicate2


title: SA8

description:
Sample name: 8
Secreted proteins


title: E171_24h_biologicalreplicate3_duplicate1


title: Control_E171_0h_biologicalreplicate3_duplicate1


title: Control_MPs_0h_biologicalreplicate1_duplicate1_2


title: E171_24h_biologicalreplicate3_duplicate2


title: Control_MPs_0h_biologicalreplicate2_duplicate2


title: E171_24h_biologicalreplicate1_duplicate1


title: DRG_naive_4wk_rep1


title: MPs_24h_biologicalreplicate2_duplicate2


title: Control_MPs_24h_biologicalreplicate1_duplicate1


title: MPs_24h_biologicalreplicate3_duplicate1


title: SA4

description:
Sample name: 4
Secreted proteins


title: SA5

description:
Sample name: 5
Secreted proteins


title: Control_E171_0h_biologicalreplicate2_duplicate2


title: SA1

description:
Sample name: 1
Secreted proteins


title: SA2

description:
Sample name: 2
Secreted proteins


title: SA3

description:
Sample name: 3
Secreted proteins


title: Control_E171_0h_biologicalreplicate2_duplicate1


title: SA7

description:
Sample name: 7
Secreted proteins


title: E171_24h_biologicalreplicate2_duplicate2


title: MPs_24h_biologicalreplicate2_duplicate1


title: Sample73_606934: D00000000206765_DAY 1_Tofacitinib

city: New York

first: Lewis

middle: Elwood

last: Tomalin

state: New York

address: 303 East 71st Street, Apt1B

department: Population Health Science & Policy

institute: Icahn School of Medicine at Mount Sinai

scan_protocol: Detection and quantification of the resulting DNA sequences was performed using microfluidic real-time quantitative PCR chip (96.96, Dynamic Array IFC, Fluidigm Biomark, South San Francisco, CA).

label: oligonucleotide-labeled antibody

source_name: Blood_DAY 1_Tofacitinib

treatment_protocol: Patients were treated with either tofacitinib 10mg QD or etanercept 50mg BIW as described in ClinicalTrials.gov: NCT01241591 and Bachelez et al., 2015

tag: visit

value: DAY 1

tag: treatmentshort

value: Tofacitinib

tag: pasi

tag: tag

value: NR

tag: age

tag: platesimple

tag: plate


title: Sample75_602662: D00000000206899_WEEK 4_Etanercept

data_processing: Detection and quantification of the resulting DNA sequences was performed using microfluidic real-time quantitative PCR chip (96.96, Dynamic Array IFC, Fluidigm Biomark, South San Francisco, CA).

source_name: Blood_WEEK 4_Etanercept

value: WEEK 4

tag: treatment

value: Etanercept 50 mg BIW

value: Etanercept

value: F


title: Sample74_598428: D00000000207011_DAY 1_Tofacitinib

value: R


title: Control_MPs_0h_biologicalreplicate2_duplicate1

tag: time


title: Control_E171_0h_biologicalreplicate1_duplicate2


title: Control_NPs_2h_biologicalreplicate3_duplicate1_2


title: Control_NPs_2h_biologicalreplicate3_duplicate2_2


title: Control_MPs_0h_biologicalreplicate1_duplicate2


title: Sample72_609660: D00000000206920_WEEK 4_Etanercept


title: Control_MPs_24h_biologicalreplicate3_duplicate1


title: Control_E171_24h_biologicalreplicate3_duplicate2


title: E171_24h_biologicalreplicate2_duplicate1


title: Sample70_599304: D00000000206986_DAY 1_Tofacitinib


title: Sample69_610472: D00000000206882_DAY 1_Tofacitinib


title: Sample71_609368: D00000000206803_WEEK 4_Etanercept


title: Sample68_610436: D00000000206882_WEEK 4_Tofacitinib

source_name: Blood_WEEK 4_Tofacitinib


title: Sample66_602746: D00000000206979_DAY 1_Tofacitinib


title: E171_24h_biologicalreplicate1_duplicate2


title: Control_MPs_24h_biologicalreplicate2_duplicate2


title: Control_E171_0h_biologicalreplicate1_duplicate1


title: MPs_24h_biologicalreplicate1_duplicate2


title: Sample65_607338: D00000000206775_DAY 1_Tofacitinib


title: Sample63_596544: D00000000206767_DAY 1_Tofacitinib


title: Sample64_597684: D00000000206921_WEEK 4_Tofacitinib


title: Sample62_595582: D00000000206812_WEEK 4_Etanercept


title: Sample61_601134: D00000000206910_DAY 1_Etanercept

source_name: Blood_DAY 1_Etanercept


title: Control_NPs_4h_biologicalreplicate2_duplicate2


title: Sample57_596402: D00000000207008_WEEK 4_Tofacitinib


title: Sample56_602694: D00000000206979_WEEK 4_Tofacitinib


title: Sample55_600870: D00000000207011_WEEK 4_Tofacitinib


title: Sample54_598364: D00000000206830_WEEK 4_Etanercept


title: Control_NPs_4h_biologicalreplicate1_duplicate1


title: Sample60_595768: D00000000206821_WEEK 4_Etanercept


title: Sample53_599292: D00000000206844_DAY 1_Tofacitinib


title: Sample52_585778: D00000000206812_DAY 1_Etanercept


title: NPs_24h_biologicalreplicate3_duplicate2

value: NPs


title: NPs_24h_biologicalreplicate3_duplicate1


title: SA6

description:
Sample name: 6
Secreted proteins

tag: tissue

value: serum

tag: cohort

tag: condition


title: Sample51_601262: D00000000206844_WEEK 4_Tofacitinib

value: M


title: Sample50_609386: D00000000206803_DAY 1_Etanercept


title: Sample49_601850: D00000000206946_DAY 1_Etanercept


title: NPs_4h_biologicalreplicate3_duplicate2


title: Control_NPs_24h_biologicalreplicate3_duplicate2


title: NPs_2h_biologicalreplicate3_duplicate2


title: NPs_4h_biologicalreplicate3_duplicate1


title: Control_NPs_24h_biologicalreplicate3_duplicate1


title: Sample47_599122: D00000000206976_DAY 1_Tofacitinib


title: Control_NPs_4h_biologicalreplicate3_duplicate1


title: Control_NPs_4h_biologicalreplicate3_duplicate2


title: Control_NPs_24h_biologicalreplicate2_duplicate2


title: NPs_24h_biologicalreplicate2_duplicate2


title: Sample46_606884: D00000000206837_WEEK 4_Etanercept


title: DRG_naive_8wk_rep2

tag: strain


title: Sample45_596590: D00000000206873_DAY 1_Etanercept


title: Sample44_600336: D00000000206961_DAY 1_Tofacitinib


title: Sample41_603106: D00000000206935_WEEK 4_Tofacitinib


title: Sample42_609678: D00000000206920_DAY 1_Etanercept


title: Sample39_589420: D00000000206799_DAY 1_Tofacitinib


title: Sample37_597454: D00000000206947_DAY 1_Etanercept


title: NPs_4h_biologicalreplicate2_duplicate2


title: NPs_24h_biologicalreplicate2_duplicate1


title: Control_NPs_2h_biologicalreplicate3_duplicate1


title: Control_NPs_24h_biologicalreplicate2_duplicate1


title: Sample36_597920: D00000000206947_WEEK 4_Etanercept


title: NPs_2h_biologicalreplicate3_duplicate1


title: Sample33_599024: D00000000206921_DAY 1_Tofacitinib


title: Sample31_600858: D00000000206931_WEEK 4_Etanercept


title: Sample32_596456: D00000000207008_DAY 1_Tofacitinib


title: NPs_4h_biologicalreplicate2_duplicate1


title: SA20

description:
Sample name: 20
Secreted proteins


title: Sample30_596402: D00000000207008_WEEK 4_Tofacitinib


title: Sample43_599320: D00000000206961_WEEK 4_Tofacitinib


title: Sample40_596532: D00000000206767_WEEK 4_Tofacitinib


title: NPs_2h_biologicalreplicate2_duplicate1


title: NPs_24h_biologicalreplicate1_duplicate2


title: Control_NPs_2h_biologicalreplicate2_duplicate2


title: NPs_2h_biologicalreplicate1_duplicate2


title: Control_NPs_2h_biologicalreplicate2_duplicate1


title: Control_NPs_4h_biologicalreplicate2_duplicate1


title: Sample27_600646: D00000000206976_WEEK 4_Tofacitinib


title: Control_NPs_2h_biologicalreplicate1_duplicate2


title: Sample24_601240: D00000000206910_WEEK 4_Etanercept


title: Sample26_606912: D00000000206837_DAY 1_Etanercept


title: NPs_4h_biologicalreplicate1_duplicate2


title: Sample23_607168: D00000000206789_WEEK 4_Etanercept


title: Sample35_600598: D00000000206935_DAY 1_Tofacitinib


title: Sample22_609786: D00000000206950_DAY 1_Etanercept


title: Sample21_600324: D00000000206945_WEEK 4_Etanercept


title: Sample20_596566: D00000000206873_WEEK 4_Etanercept


title: Sample95_595582: D00000000206812_WEEK 4_Etanercept


title: NPs_2h_biologicalreplicate2_duplicate2


title: Sample94_596664: D00000000206964_WEEK 4_Etanercept


title: Control_NPs_4h_biologicalreplicate1_duplicate2


title: Sample18_596528: D00000000206899_DAY 1_Etanercept


title: Control_NPs_24h_biologicalreplicate1_duplicate1


title: Sample17_610004: D00000000206950_WEEK 4_Etanercept


title: NPs_2h_biologicalreplicate1_duplicate1


title: NPs_24h_biologicalreplicate1_duplicate1


title: Control_NPs_2h_biologicalreplicate1_duplicate1


title: Sample16_607614: D00000000206765_WEEK 4_Tofacitinib


title: Sample93_584838: D00000000206986_WEEK 4_Tofacitinib


title: Sample92_602746: D00000000206979_DAY 1_Tofacitinib


title: Sample91_601622: D00000000206891_WEEK 4_Tofacitinib


title: NPs_4h_biologicalreplicate1_duplicate1


title: Sample13_602618: D00000000206830_DAY 1_Etanercept


title: Sample15_599288: D00000000206939_DAY 1_Tofacitinib


title: Sample11_607166: D00000000206789_DAY 1_Etanercept


title: Sample12_602732: D00000000206946_WEEK 4_Etanercept


title: Control_MPs_24h_biologicalreplicate3_duplicate2


title: Sample14_597604: D00000000206821_DAY 1_Etanercept


title: Sample89_585778: D00000000206812_DAY 1_Etanercept


title: Sample88_600858: D00000000206931_WEEK 4_Etanercept


title: Sample90_596456: D00000000207008_DAY 1_Tofacitinib


title: Sample87_600646: D00000000206976_WEEK 4_Tofacitinib


title: Sample86_609660: D00000000206920_WEEK 4_Etanercept


title: Sample10_607316: D00000000206775_WEEK 4_Tofacitinib


title: Sample85_599292: D00000000206844_DAY 1_Tofacitinib


title: Sample83_595760: D00000000206780_WEEK 4_Tofacitinib


title: Sample9_596456: D00000000207008_DAY 1_Tofacitinib


title: Sample82_596566: D00000000206873_WEEK 4_Etanercept


title: Sample81_599190: D00000000206836_WEEK 4_Etanercept


title: Sample6_602094: D00000000206945_DAY 1_Etanercept


title: Sample5_598424: D00000000206968_WEEK 4_Etanercept


title: Sample8_585403: D00000000206939_WEEK 4_Tofacitinib


title: Sample79_607022: D00000000206868_DAY 1_Etanercept


title: Sample7_597938: D00000000206793_DAY 1_Etanercept


title: Sample80_609786: D00000000206950_DAY 1_Etanercept


title: Sample78_602732: D00000000206946_WEEK 4_Etanercept


title: Sample77_596528: D00000000206899_DAY 1_Etanercept


title: Sample2_598984: D00000000206931_DAY 1_Etanercept


title: Sample76_601240: D00000000206910_WEEK 4_Etanercept


title: Sample1_585734: D00000000206793_WEEK 4_Etanercept


title: Sample94_600854: D00000000206715_WEEK 4_Etanercept


title: Sample74_602610: D00000000206805_WEEK 4_Tofacitinib


title: Sample73_603220: D00000000206780_DAY 1_Tofacitinib


title: Sample29_601664: D00000000206805_DAY 1_Tofacitinib


title: Sample92_610132: D00000000206647_DAY 1_Tofacitinib


title: Sample71_599122: D00000000206976_DAY 1_Tofacitinib


title: Control_MPs_0h_biologicalreplicate1_duplicate1


title: Sample70_601664: D00000000206805_DAY 1_Tofacitinib


title: Sample69_599280: D00000000206982_WEEK 4_Tofacitinib


title: Sample4_602090: D00000000206799_WEEK 4_Tofacitinib


title: Sample89_609382: D00000000206764_DAY 1_Tofacitinib


title: Sample3_601258: D00000000206968_DAY 1_Etanercept


title: Sample68_610472: D00000000206882_DAY 1_Tofacitinib


title: Sample86_601234: D00000000206723_WEEK 4_Tofacitinib


title: Sample88_585637: D00000000206674_WEEK 4_Etanercept


title: Sample75_607316: D00000000206775_WEEK 4_Tofacitinib


title: Sample85_609456: D00000000206530_WEEK 4_Tofacitinib


title: Sample65_607614: D00000000206765_WEEK 4_Tofacitinib


title: Sample91_598384: D00000000206663_DAY 1_Etanercept


title: Sample93_596336: D00000000206566_WEEK 4_Tofacitinib


title: Sample64_596402: D00000000207008_WEEK 4_Tofacitinib


title: Sample83_603188: D00000000206561_WEEK 4_Etanercept


title: Sample90_596308: D00000000206728_WEEK 4_Tofacitinib


title: Sample62_601292: D00000000206891_DAY 1_Tofacitinib


title: Sample81_609974: D00000000206707_DAY 1_Tofacitinib


title: Sample61_596590: D00000000206873_DAY 1_Etanercept


title: Sample58_602094: D00000000206945_DAY 1_Etanercept


title: Sample80_600480: D00000000206561_DAY 1_Etanercept


title: Sample82_602614: D00000000206723_DAY 1_Tofacitinib


title: Sample57_601134: D00000000206910_DAY 1_Etanercept


title: Sample66_600336: D00000000206961_DAY 1_Tofacitinib


title: Sample77_597430: D00000000206533_DAY 1_Tofacitinib


title: Sample56_609368: D00000000206803_WEEK 4_Etanercept


title: Sample78_600488: D00000000206655_DAY 1_Etanercept


title: Sample75_607170: D00000000206545_WEEK 4_Tofacitinib


title: Sample54_600324: D00000000206945_WEEK 4_Etanercept


title: Sample55_597938: D00000000206793_DAY 1_Etanercept


title: Sample67_599088: D00000000206955_WEEK 4_Tofacitinib


title: Sample76_600400: D00000000206746_WEEK 4_Tofacitinib


title: Sample79_601832: D00000000206714_WEEK 4_Etanercept


title: Sample52_599116: D00000000206839_DAY 1_Etanercept


title: Sample63_610004: D00000000206950_WEEK 4_Etanercept


title: Sample70_602722: D00000000206692_DAY 1_Etanercept


title: Sample69_589001: D00000000206596_DAY 1_Etanercept


title: Sample71_607292: D00000000206536_WEEK 4_Tofacitinib


title: Sample50_607338: D00000000206775_DAY 1_Tofacitinib


title: Sample51_599024: D00000000206921_DAY 1_Tofacitinib


title: Sample49_598424: D00000000206968_WEEK 4_Etanercept


title: Sample68_609548: D00000000206690_WEEK 4_Etanercept


title: Sample46_599320: D00000000206961_WEEK 4_Tofacitinib


title: Sample45_602694: D00000000206979_WEEK 4_Tofacitinib


title: Sample65_603084: D00000000206537_WEEK 4_Etanercept


title: Sample87_607604: D00000000206720_WEEK 4_Tofacitinib


title: Sample66_597768: D00000000206722_WEEK 4_Tofacitinib


title: Sample43_597604: D00000000206821_DAY 1_Etanercept


title: Sample73_600944: D00000000206636_WEEK 4_Etanercept


title: Sample53_600638: D00000000206964_DAY 1_Etanercept


title: Sample64_610400: D00000000206588_WEEK 4_Tofacitinib


title: Sample41_599288: D00000000206939_DAY 1_Tofacitinib


title: Sample61_589454: D00000000206759_DAY 1_Etanercept


title: Sample40_601262: D00000000206844_WEEK 4_Tofacitinib


title: Sample62_599104: D00000000206698_WEEK 4_Tofacitinib


title: Sample59_607618: D00000000206720_DAY 1_Tofacitinib


title: Sample42_589420: D00000000206799_DAY 1_Tofacitinib


title: Sample58_597512: D00000000206649_WEEK 4_Tofacitinib


title: Sample38_596494: D00000000206838_DAY 1_Etanercept


title: Sample67_606864: D00000000206624_WEEK 4_Etanercept


title: Sample47_606934: D00000000206765_DAY 1_Tofacitinib


title: Sample63_598352: D00000000206663_WEEK 4_Etanercept


title: Sample37_598984: D00000000206931_DAY 1_Etanercept


title: Sample57_601674: D00000000206596_WEEK 4_Etanercept


title: Sample35_598734: D00000000206955_DAY 1_Tofacitinib


title: Sample34_602662: D00000000206899_WEEK 4_Etanercept


title: Sample44_598460: D00000000206911_WEEK 4_Tofacitinib


title: Sample54_601648: D00000000206748_WEEK 4_Tofacitinib


title: Sample33_607168: D00000000206789_WEEK 4_Etanercept


title: Sample53_598446: D00000000206748_DAY 1_Tofacitinib


title: Control_NPs_24h_biologicalreplicate1_duplicate2


title: Sample32_609386: D00000000206803_DAY 1_Etanercept


title: Sample39_597920: D00000000206947_WEEK 4_Etanercept


title: Sample52_596358: D00000000206542_DAY 1_Tofacitinib


title: Sample51_609496: D00000000206530_DAY 1_Tofacitinib


title: Sample30_597684: D00000000206921_WEEK 4_Tofacitinib


title: Sample49_609704: D00000000206764_WEEK 4_Tofacitinib


title: Sample29_601258: D00000000206968_DAY 1_Etanercept


title: Sample28_602090: D00000000206799_WEEK 4_Tofacitinib


title: Sample27_602618: D00000000206830_DAY 1_Etanercept


title: Sample47_597528: D00000000206598_DAY 1_Tofacitinib


title: Sample26_598428: D00000000207011_DAY 1_Tofacitinib


title: Sample25_600458: D00000000206982_DAY 1_Tofacitinib


title: Sample55_607008: D00000000206624_DAY 1_Etanercept


title: Sample43_600812: D00000000206649_DAY 1_Tofacitinib


title: Sample45_596660: D00000000206550_DAY 1_Tofacitinib


title: Sample24_596532: D00000000206767_WEEK 4_Tofacitinib


title: Sample23_610436: D00000000206882_WEEK 4_Tofacitinib


title: Sample22_610476: D00000000206887_WEEK 4_Tofacitinib


title: Sample42_595474: D00000000206762_WEEK 4_Tofacitinib


title: Sample41_609638: D00000000206690_DAY 1_Etanercept


title: Sample56_601166: D00000000206725_DAY 1_Etanercept


title: Sample40_595790: D00000000206684_WEEK 4_Tofacitinib


title: Sample31_589914: D00000000206768_DAY 1_Etanercept


title: Sample39_596390: D00000000206745_DAY 1_Tofacitinib


title: Sample50_599338: D00000000206550_WEEK 4_Tofacitinib


title: Sample21_595768: D00000000206821_WEEK 4_Etanercept


title: Sample46_602220: D00000000206746_DAY 1_Tofacitinib


title: Sample18_585734: D00000000206793_WEEK 4_Etanercept


title: Sample37_595868: D00000000206722_DAY 1_Tofacitinib


title: Sample35_597660: D00000000206684_DAY 1_Tofacitinib


title: Sample34_607326: D00000000206536_DAY 1_Tofacitinib


title: Sample33_598858: D00000000206612_DAY 1_Etanercept


title: Sample15_600870: D00000000207011_WEEK 4_Tofacitinib


title: Sample17_597454: D00000000206947_DAY 1_Etanercept


title: Sample16_588673: D00000000206768_WEEK 4_Etanercept


title: Sample31_609604: D00000000206639_WEEK 4_Etanercept


title: Sample32_596374: D00000000206728_DAY 1_Tofacitinib


title: Sample14_602088: D00000000206836_DAY 1_Etanercept


title: Sample30_598968: D00000000206715_DAY 1_Etanercept


title: Sample20_606924: D00000000206868_WEEK 4_Etanercept


title: Sample29_590208: D00000000206672_DAY 1_Etanercept


title: Sample38_598908: D00000000206698_DAY 1_Tofacitinib


title: Sample13_602604: D00000000206838_WEEK 4_Etanercept


title: Sample11_600640: D00000000206839_WEEK 4_Etanercept


title: Sample12_602592: D00000000206911_DAY 1_Tofacitinib


title: Sample28_610340: D00000000206588_DAY 1_Tofacitinib


title: Sample19_596544: D00000000206767_DAY 1_Tofacitinib


title: Sample8_607166: D00000000206789_DAY 1_Etanercept


title: Sample9_606884: D00000000206837_WEEK 4_Etanercept


title: Sample7_585403: D00000000206939_WEEK 4_Tofacitinib


title: Sample25_600690: D00000000206688_DAY 1_Tofacitinib


title: Sample24_606862: D00000000206740_WEEK 4_Etanercept


title: Sample26_589440: D00000000206742_DAY 1_Etanercept


title: Sample5_598364: D00000000206830_WEEK 4_Etanercept


title: Sample6_606912: D00000000206837_DAY 1_Etanercept


title: Sample3_601850: D00000000206946_DAY 1_Etanercept


title: Sample23_596296: D00000000206676_DAY 1_Etanercept


title: Sample22_601792: D00000000206725_WEEK 4_Etanercept


title: Sample21_602076: D00000000206742_WEEK 4_Etanercept


title: Sample1_603106: D00000000206935_WEEK 4_Tofacitinib


title: Sample2_599304: D00000000206986_DAY 1_Tofacitinib


title: Sample19_598752: D00000000206745_WEEK 4_Tofacitinib


title: Sample20_601158: D00000000206714_DAY 1_Etanercept


title: Sample27_602368: D00000000206672_WEEK 4_Etanercept


title: Sample95_603022: D00000000206655_WEEK 4_Etanercept


title: Sample91_598384: D00000000206663_DAY 1_Etanercept


title: Sample93_596336: D00000000206566_WEEK 4_Tofacitinib


title: Sample90_596308: D00000000206728_WEEK 4_Tofacitinib


title: Sample94_600854: D00000000206715_WEEK 4_Etanercept


title: Sample14_596548: D00000000206566_DAY 1_Tofacitinib


title: Sample13_601668: D00000000206762_DAY 1_Tofacitinib


title: Sample92_610132: D00000000206647_DAY 1_Tofacitinib


title: Sample16_598444: D00000000206692_WEEK 4_Etanercept


title: Sample18_600496: D00000000206537_DAY 1_Etanercept


title: Sample17_597896: D00000000206533_WEEK 4_Tofacitinib


title: Sample15_601048: D00000000206613_WEEK 4_Tofacitinib


title: Sample88_585637: D00000000206674_WEEK 4_Etanercept


title: Sample87_607604: D00000000206720_WEEK 4_Tofacitinib


title: Sample86_601234: D00000000206723_WEEK 4_Tofacitinib


title: Sample12_599108: D00000000206613_DAY 1_Tofacitinib


title: Sample85_609456: D00000000206530_WEEK 4_Tofacitinib


title: Sample9_602716: D00000000206676_WEEK 4_Etanercept


title: Sample8_596384: D00000000206542_WEEK 4_Tofacitinib


title: Sample10_606906: D00000000206740_DAY 1_Etanercept


title: Sample83_603188: D00000000206561_WEEK 4_Etanercept


title: Sample82_602614: D00000000206723_DAY 1_Tofacitinib


title: Sample6_609608: D00000000206639_DAY 1_Etanercept


title: Sample7_599228: D00000000206598_WEEK 4_Tofacitinib


title: Sample5_597894: D00000000206688_WEEK 4_Tofacitinib


title: Sample80_600480: D00000000206561_DAY 1_Etanercept


title: Sample81_609974: D00000000206707_DAY 1_Tofacitinib


title: Sample4_610112: D00000000206647_WEEK 4_Tofacitinib


title: Sample89_609382: D00000000206764_DAY 1_Tofacitinib


title: Sample2_602180: D00000000206759_WEEK 4_Etanercept


title: Sample3_607184: D00000000206545_DAY 1_Tofacitinib


title: Sample93_601718: D00000000206473_DAY 1_Etanercept


title: Sample78_600488: D00000000206655_DAY 1_Etanercept


title: Sample79_601832: D00000000206714_WEEK 4_Etanercept


title: Sample77_597430: D00000000206533_DAY 1_Tofacitinib


title: Sample76_600400: D00000000206746_WEEK 4_Tofacitinib


title: Sample95_602336: D00000000206529_DAY 1_Tofacitinib


title: Sample73_600944: D00000000206636_WEEK 4_Etanercept


title: Sample74_599184: D00000000206674_DAY 1_Etanercept


title: Sample92_597580: D00000000206526_DAY 1_Tofacitinib


title: Sample75_607170: D00000000206545_WEEK 4_Tofacitinib


title: Sample69_589001: D00000000206596_DAY 1_Etanercept


title: Sample71_607292: D00000000206536_WEEK 4_Tofacitinib


title: Sample70_602722: D00000000206692_DAY 1_Etanercept


title: Sample91_595490: D00000000206473_WEEK 4_Etanercept


title: Sample90_590018: D00000000206484_DAY 1_Tofacitinib


title: Sample68_609548: D00000000206690_WEEK 4_Etanercept


title: Sample88_595732: D00000000206522_DAY 1_Tofacitinib


title: Sample89_600300: D00000000206487_WEEK 4_Etanercept


title: Sample87_596516: D00000000206461_WEEK 4_Tofacitinib


title: Sample67_606864: D00000000206624_WEEK 4_Etanercept


title: Sample86_602526: D00000000206375_WEEK 4_Etanercept


title: Sample85_599056: D00000000206385_WEEK 4_Tofacitinib


title: Sample66_597768: D00000000206722_WEEK 4_Tofacitinib


title: Sample64_610400: D00000000206588_WEEK 4_Tofacitinib


title: Sample65_603084: D00000000206537_WEEK 4_Etanercept


title: Sample83_600884: D00000000206506_WEEK 4_Etanercept


title: Sample62_599104: D00000000206698_WEEK 4_Tofacitinib


title: Sample81_601680: D00000000206499_DAY 1_Tofacitinib


title: Sample63_598352: D00000000206663_WEEK 4_Etanercept


title: Sample79_599050: D00000000206507_WEEK 4_Etanercept


title: Sample80_607490: D00000000206469_WEEK 4_Tofacitinib


title: Sample61_589454: D00000000206759_DAY 1_Etanercept


title: Sample82_609362: D00000000206456_DAY 1_Tofacitinib


title: Sample58_597512: D00000000206649_WEEK 4_Tofacitinib


title: Sample78_597740: D00000000206487_DAY 1_Etanercept


title: Sample57_601674: D00000000206596_WEEK 4_Etanercept


title: Sample76_597714: D00000000206521_DAY 1_Etanercept


title: Sample59_607618: D00000000206720_DAY 1_Tofacitinib


title: Sample77_609902: D00000000206353_WEEK 4_Etanercept


title: Sample56_601166: D00000000206725_DAY 1_Etanercept


title: Sample75_596478: D00000000206411_DAY 1_Tofacitinib


title: Sample73_599140: D00000000206439_WEEK 4_Tofacitinib


title: Sample53_598446: D00000000206748_DAY 1_Tofacitinib


title: Sample54_601648: D00000000206748_WEEK 4_Tofacitinib


title: Sample55_607008: D00000000206624_DAY 1_Etanercept


title: Sample71_602080: D00000000206484_WEEK 4_Tofacitinib


title: Sample70_585160: D00000000206398_WEEK 4_Etanercept


title: Sample69_597398: D00000000206382_WEEK 4_Etanercept


title: Sample51_609496: D00000000206530_DAY 1_Tofacitinib


title: Sample74_596366: D00000000206411_WEEK 4_Tofacitinib


title: Sample50_599338: D00000000206550_WEEK 4_Tofacitinib


title: Sample52_596358: D00000000206542_DAY 1_Tofacitinib


title: Sample49_609704: D00000000206764_WEEK 4_Tofacitinib


title: Sample68_609730: D00000000206320_WEEK 4_Etanercept


title: Sample67_609712: D00000000206320_DAY 1_Etanercept


title: Sample46_602220: D00000000206746_DAY 1_Tofacitinib


title: Sample47_597528: D00000000206598_DAY 1_Tofacitinib


title: Sample45_596660: D00000000206550_DAY 1_Tofacitinib


title: Sample64_599078: D00000000206506_DAY 1_Etanercept


title: Sample65_596498: D00000000206383_DAY 1_Etanercept


title: Sample44_598768: D00000000206636_DAY 1_Etanercept


title: Sample63_602110: D00000000206360_WEEK 4_Tofacitinib


title: Sample43_600812: D00000000206649_DAY 1_Tofacitinib


title: Sample61_600862: D00000000206477_DAY 1_Etanercept


title: Sample42_595474: D00000000206762_WEEK 4_Tofacitinib


title: Sample40_595790: D00000000206684_WEEK 4_Tofacitinib


title: Sample59_599260: D00000000206379_DAY 1_Tofacitinib


title: Sample1_602194: D00000000206612_WEEK 4_Etanercept


title: Sample62_598416: D00000000206410_WEEK 4_Etanercept


title: Sample57_609488: D00000000206447_DAY 1_Etanercept


title: Sample38_598908: D00000000206698_DAY 1_Tofacitinib


title: Sample56_596344: D00000000206383_WEEK 4_Etanercept


title: Sample34_607326: D00000000206536_DAY 1_Tofacitinib


title: Sample58_609428: D00000000206517_WEEK 4_Tofacitinib


title: Sample35_597660: D00000000206684_DAY 1_Tofacitinib


title: Sample55_609360: D00000000206513_WEEK 4_Tofacitinib


title: Sample54_607470: D00000000206464_WEEK 4_Tofacitinib


title: Sample66_595712: D00000000206521_WEEK 4_Etanercept


title: Sample51_602296: D00000000206432_DAY 1_Etanercept


title: Sample52_601662: D00000000206325_DAY 1_Etanercept


title: Sample39_596390: D00000000206745_DAY 1_Tofacitinib


title: Sample33_598858: D00000000206612_DAY 1_Etanercept


title: Sample32_596374: D00000000206728_DAY 1_Tofacitinib


title: Sample41_609638: D00000000206690_DAY 1_Etanercept


title: Sample50_603662: D00000000206360_DAY 1_Tofacitinib


title: Sample31_609604: D00000000206639_WEEK 4_Etanercept


title: Sample49_599146: D00000000206458_WEEK 4_Etanercept


title: Sample46_598976: D00000000206522_WEEK 4_Tofacitinib


title: Sample29_590208: D00000000206672_DAY 1_Etanercept


title: Sample30_598968: D00000000206715_DAY 1_Etanercept


title: Sample47_590266: D00000000206479_DAY 1_Etanercept


title: Sample45_599222: D00000000206403_WEEK 4_Etanercept


title: Sample37_595868: D00000000206722_DAY 1_Tofacitinib


title: Sample28_610340: D00000000206588_DAY 1_Tofacitinib


title: Sample25_600690: D00000000206688_DAY 1_Tofacitinib


title: Sample27_602368: D00000000206672_WEEK 4_Etanercept


title: Sample42_600790: D00000000206435_DAY 1_Tofacitinib


title: Sample24_606862: D00000000206740_WEEK 4_Etanercept


title: Sample26_589440: D00000000206742_DAY 1_Etanercept


title: Sample41_599102: D00000000206356_WEEK 4_Etanercept


title: Sample43_599216: D00000000206529_WEEK 4_Tofacitinib


title: Sample22_601792: D00000000206725_WEEK 4_Etanercept


title: Sample23_596296: D00000000206676_DAY 1_Etanercept


title: Sample39_603098: D00000000206422_WEEK 4_Etanercept


title: Sample40_602024: D00000000206512_DAY 1_Etanercept


title: Sample20_601158: D00000000206714_DAY 1_Etanercept


title: Sample21_602076: D00000000206742_WEEK 4_Etanercept


title: Sample37_607496: D00000000206380_WEEK 4_Etanercept


title: Sample35_602616: D00000000206410_DAY 1_Etanercept


title: Sample18_600496: D00000000206537_DAY 1_Etanercept


title: Sample38_602200: D00000000206477_WEEK 4_Etanercept


title: Sample19_598752: D00000000206745_WEEK 4_Tofacitinib


title: Sample44_600514: D00000000206467_WEEK 4_Etanercept


title: Sample34_602554: D00000000206479_WEEK 4_Etanercept


title: Sample15_601048: D00000000206613_WEEK 4_Tofacitinib


title: Sample17_597896: D00000000206533_WEEK 4_Tofacitinib


title: Sample16_598444: D00000000206692_WEEK 4_Etanercept


title: Sample33_610324: D00000000206468_WEEK 4_Etanercept


title: Sample32_585604: D00000000206379_WEEK 4_Tofacitinib


title: Sample31_599218: D00000000206398_DAY 1_Etanercept


title: Sample14_596548: D00000000206566_DAY 1_Tofacitinib


title: Sample30_598986: D00000000206373_WEEK 4_Tofacitinib


title: Sample29_607252: D00000000206380_DAY 1_Etanercept


title: Sample12_599108: D00000000206613_DAY 1_Tofacitinib


title: Sample28_598732: D00000000206452_DAY 1_Tofacitinib


title: Sample11_610078: D00000000206707_WEEK 4_Tofacitinib


title: Sample9_602716: D00000000206676_WEEK 4_Etanercept


title: Sample13_601668: D00000000206762_DAY 1_Tofacitinib


title: Sample8_596384: D00000000206542_WEEK 4_Tofacitinib


title: Sample27_607182: D00000000206469_DAY 1_Tofacitinib


title: Sample25_609466: D00000000206517_DAY 1_Tofacitinib


title: Sample26_602774: D00000000206499_WEEK 4_Tofacitinib


title: Sample6_609608: D00000000206639_DAY 1_Etanercept


title: Sample5_597894: D00000000206688_WEEK 4_Tofacitinib


title: Sample7_599228: D00000000206598_WEEK 4_Tofacitinib


title: Sample24_606986: D00000000206500_DAY 1_Tofacitinib


title: Sample21_597678: D00000000206403_DAY 1_Etanercept


title: Sample22_603654: D00000000206373_DAY 1_Tofacitinib


title: Sample20_595588: D00000000206325_WEEK 4_Etanercept


title: Sample2_602180: D00000000206759_WEEK 4_Etanercept


title: Sample18_598970: D00000000206385_DAY 1_Tofacitinib


title: Sample16_598990: D00000000206375_DAY 1_Etanercept


title: Sample95_602336: D00000000206529_DAY 1_Tofacitinib


title: Sample19_600806: D00000000206382_DAY 1_Etanercept


title: Sample15_603696: D00000000206526_WEEK 4_Tofacitinib


title: Sample94_602098: D00000000206432_WEEK 4_Etanercept


title: Sample93_601718: D00000000206473_DAY 1_Etanercept


title: Sample3_607184: D00000000206545_DAY 1_Tofacitinib


title: Sample91_595490: D00000000206473_WEEK 4_Etanercept


title: Sample1_602194: D00000000206612_WEEK 4_Etanercept


title: Sample92_597580: D00000000206526_DAY 1_Tofacitinib


title: Sample14_600340: D00000000206512_WEEK 4_Etanercept


title: Sample89_600300: D00000000206487_WEEK 4_Etanercept


title: Sample23_598878: D00000000206439_DAY 1_Tofacitinib


title: Sample17_598718: D00000000206356_DAY 1_Etanercept


title: Sample7_597886: D00000000206435_WEEK 4_Tofacitinib


title: Sample90_590018: D00000000206484_DAY 1_Tofacitinib


title: Sample4_610112: D00000000206647_WEEK 4_Tofacitinib


title: Sample13_598822: D00000000206458_DAY 1_Etanercept


title: Sample12_602206: D00000000206467_DAY 1_Etanercept


title: Sample88_595732: D00000000206522_DAY 1_Tofacitinib


title: Sample10_607602: D00000000206464_DAY 1_Tofacitinib


title: Sample87_596516: D00000000206461_WEEK 4_Tofacitinib


title: Sample86_602526: D00000000206375_WEEK 4_Etanercept


title: Sample9_599036: D00000000206452_WEEK 4_Tofacitinib


title: Sample79_599050: D00000000206507_WEEK 4_Etanercept


title: Sample8_600582: D00000000206422_DAY 1_Etanercept


title: Sample78_597740: D00000000206487_DAY 1_Etanercept


title: Sample77_609902: D00000000206353_WEEK 4_Etanercept


title: Sample92_585318: D00000000206064_WEEK 4_Tofacitinib


title: Sample93_599072: D00000000206156_DAY 1_Tofacitinib


title: Sample6_606920: D00000000206500_WEEK 4_Tofacitinib


title: Sample85_599056: D00000000206385_WEEK 4_Tofacitinib


title: Sample11_609492: D00000000206353_DAY 1_Etanercept


title: Sample4_609344: D00000000206456_WEEK 4_Tofacitinib


title: Sample81_601680: D00000000206499_DAY 1_Tofacitinib


title: Sample90_595806: D00000000206217_WEEK 4_Tofacitinib


title: Sample80_607490: D00000000206469_WEEK 4_Tofacitinib


title: Sample82_609362: D00000000206456_DAY 1_Tofacitinib


title: Sample95_596302: D00000000206286_WEEK 4_Tofacitinib


title: Sample89_589518: D00000000206215_DAY 1_Tofacitinib


title: Sample87_599254: D00000000206046_WEEK 4_Tofacitinib


title: Sample83_600884: D00000000206506_WEEK 4_Etanercept


title: Sample1_598682: D00000000206507_DAY 1_Etanercept


title: Sample74_596366: D00000000206411_WEEK 4_Tofacitinib


title: Sample75_596478: D00000000206411_DAY 1_Tofacitinib


title: Sample86_609576: D00000000206123_WEEK 4_Etanercept


title: Sample73_599140: D00000000206439_WEEK 4_Tofacitinib


title: Sample70_585160: D00000000206398_WEEK 4_Etanercept


title: Sample76_597714: D00000000206521_DAY 1_Etanercept


title: Sample88_602256: D00000000206274_DAY 1_Tofacitinib


title: Sample85_596696: D00000000206254_DAY 1_Etanercept


title: Sample69_597398: D00000000206382_WEEK 4_Etanercept


title: Sample82_596252: D00000000206131_DAY 1_Etanercept


title: Sample67_609712: D00000000206320_DAY 1_Etanercept


title: Sample81_598758: D00000000206113_DAY 1_Etanercept


title: Sample65_596498: D00000000206383_DAY 1_Etanercept


title: Sample80_602584: D00000000206147_WEEK 4_Etanercept


title: Sample64_599078: D00000000206506_DAY 1_Etanercept


title: Sample63_602110: D00000000206360_WEEK 4_Tofacitinib


title: Sample78_610084: D00000000206284_WEEK 4_Etanercept


title: Sample71_602080: D00000000206484_WEEK 4_Tofacitinib


title: Sample62_598416: D00000000206410_WEEK 4_Etanercept


title: Sample76_599134: D00000000206113_WEEK 4_Etanercept


title: Sample66_595712: D00000000206521_WEEK 4_Etanercept


title: Sample79_599318: D00000000206221_DAY 1_Etanercept


title: Sample75_597798: D00000000206033_DAY 1_Tofacitinib


title: Sample83_602624: D00000000206050_WEEK 4_Tofacitinib


title: Sample74_599066: D00000000206086_DAY 1_Tofacitinib


title: Sample58_609428: D00000000206517_WEEK 4_Tofacitinib


title: Sample68_609730: D00000000206320_WEEK 4_Etanercept


title: Sample71_600378: D00000000206241_DAY 1_Tofacitinib


title: Sample59_599260: D00000000206379_DAY 1_Tofacitinib


title: Sample3_596320: D00000000206461_DAY 1_Tofacitinib


title: Sample70_602598: D00000000206232_WEEK 4_Tofacitinib


title: Sample69_603060: D00000000206042_WEEK 4_Etanercept


title: Sample55_609360: D00000000206513_WEEK 4_Tofacitinib


title: Sample56_596344: D00000000206383_WEEK 4_Etanercept


title: Sample54_607470: D00000000206464_WEEK 4_Tofacitinib


title: Sample77_597852: D00000000206121_DAY 1_Tofacitinib


title: Sample66_602650: D00000000206232_DAY 1_Tofacitinib


title: Sample67_600512: D00000000206053_DAY 1_Tofacitinib


title: Sample53_609378: D00000000206513_DAY 1_Tofacitinib


title: Sample61_600862: D00000000206477_DAY 1_Etanercept


title: Sample64_585548: D00000000206265_WEEK 4_Etanercept


title: Sample52_601662: D00000000206325_DAY 1_Etanercept


title: Sample50_603662: D00000000206360_DAY 1_Tofacitinib


title: Sample63_603008: D00000000206058_DAY 1_Tofacitinib


title: Sample57_609488: D00000000206447_DAY 1_Etanercept


title: Sample51_602296: D00000000206432_DAY 1_Etanercept


title: Sample62_609620: D00000000206123_DAY 1_Etanercept


title: Sample49_599146: D00000000206458_WEEK 4_Etanercept


title: Sample61_603206: D00000000206241_WEEK 4_Tofacitinib


title: Sample59_601006: D00000000206104_DAY 1_Etanercept


title: Sample55_599324: D00000000206109_WEEK 4_Etanercept


title: Sample58_610352: D00000000206097_DAY 1_Tofacitinib


title: Sample46_598976: D00000000206522_WEEK 4_Tofacitinib


title: Sample45_599222: D00000000206403_WEEK 4_Etanercept


title: Sample53_609450: D00000000206251_DAY 1_Etanercept


title: Sample54_609420: D00000000206251_WEEK 4_Etanercept


title: Sample44_600514: D00000000206467_WEEK 4_Etanercept


title: Sample51_600348: D00000000206100_DAY 1_Etanercept


title: Sample43_599216: D00000000206529_WEEK 4_Tofacitinib


title: Sample65_601254: D00000000206235_WEEK 4_Etanercept


title: Sample41_599102: D00000000206356_WEEK 4_Etanercept


title: Sample47_590266: D00000000206479_DAY 1_Etanercept


title: Sample40_602024: D00000000206512_DAY 1_Etanercept


title: Sample49_599186: D00000000206121_WEEK 4_Tofacitinib


title: Sample56_603680: D00000000206073_DAY 1_Etanercept


title: Sample34_602554: D00000000206479_WEEK 4_Etanercept


title: Sample45_600874: D00000000206086_WEEK 4_Tofacitinib


title: Sample47_596466: D00000000206286_DAY 1_Tofacitinib


title: Sample46_602566: D00000000206192_WEEK 4_Tofacitinib


title: Sample33_610324: D00000000206468_WEEK 4_Etanercept


title: Sample32_585604: D00000000206379_WEEK 4_Tofacitinib


title: Sample37_607496: D00000000206380_WEEK 4_Etanercept


title: Sample42_600790: D00000000206435_DAY 1_Tofacitinib


title: Sample42_609394: D00000000206266_WEEK 4_Tofacitinib


title: Sample52_603018: D00000000206053_WEEK 4_Tofacitinib


title: Sample43_597854: D00000000206064_DAY 1_Tofacitinib


title: Sample31_599218: D00000000206398_DAY 1_Etanercept


title: Sample30_598986: D00000000206373_WEEK 4_Tofacitinib


title: Sample44_609422: D00000000206266_DAY 1_Tofacitinib


title: Sample29_607252: D00000000206380_DAY 1_Etanercept


title: Sample38_602200: D00000000206477_WEEK 4_Etanercept


title: Sample39_602282: D00000000206274_WEEK 4_Tofacitinib


title: Sample39_603098: D00000000206422_WEEK 4_Etanercept


title: Sample41_589636: D00000000206213_DAY 1_Etanercept


title: Sample28_598732: D00000000206452_DAY 1_Tofacitinib


title: Sample50_597858: D00000000206217_DAY 1_Tofacitinib


title: Sample37_600846: D00000000206156_WEEK 4_Tofacitinib


title: Sample40_598792: D00000000206050_DAY 1_Tofacitinib


title: Sample27_607182: D00000000206469_DAY 1_Tofacitinib


title: Sample35_602616: D00000000206410_DAY 1_Etanercept


title: Sample25_609466: D00000000206517_DAY 1_Tofacitinib


title: Sample26_602774: D00000000206499_WEEK 4_Tofacitinib


title: Sample35_585618: D00000000205981_DAY 1_Tofacitinib


title: Sample38_597642: D00000000206104_WEEK 4_Etanercept


title: Sample22_603654: D00000000206373_DAY 1_Tofacitinib


title: Sample33_600384: D00000000206173_WEEK 4_Tofacitinib


title: Sample24_606986: D00000000206500_DAY 1_Tofacitinib


title: Sample21_597678: D00000000206403_DAY 1_Etanercept


title: Sample31_600482: D00000000206107_DAY 1_Tofacitinib


title: Sample32_599300: D00000000206033_WEEK 4_Tofacitinib


title: Sample20_595588: D00000000206325_WEEK 4_Etanercept


title: Sample29_600356: D00000000206042_DAY 1_Etanercept


title: Sample28_603006: D00000000206100_WEEK 4_Etanercept


title: Sample18_598970: D00000000206385_DAY 1_Tofacitinib


title: Sample19_600806: D00000000206382_DAY 1_Etanercept


title: Sample34_610018: D00000000206284_DAY 1_Etanercept


title: Sample27_601988: D00000000206316_WEEK 4_Tofacitinib


title: Sample30_597730: D00000000206058_WEEK 4_Tofacitinib


title: Sample15_603696: D00000000206526_WEEK 4_Tofacitinib


title: Sample16_598990: D00000000206375_DAY 1_Etanercept


title: Sample17_598718: D00000000206356_DAY 1_Etanercept


title: Sample14_600340: D00000000206512_WEEK 4_Etanercept


title: Sample12_602206: D00000000206467_DAY 1_Etanercept


title: Sample23_598878: D00000000206439_DAY 1_Tofacitinib


title: Sample24_597890: D00000000206046_DAY 1_Tofacitinib


title: Sample25_610136: D00000000206149_DAY 1_Etanercept


title: Sample22_602056: D00000000206157_WEEK 4_Tofacitinib


title: Sample23_603046: D00000000206107_WEEK 4_Tofacitinib


title: Sample26_595462: D00000000206167_WEEK 4_Etanercept


title: Sample21_602124: D00000000206173_DAY 1_Tofacitinib


title: Sample11_609492: D00000000206353_DAY 1_Etanercept


title: Sample13_598822: D00000000206458_DAY 1_Etanercept


title: Sample10_607602: D00000000206464_DAY 1_Tofacitinib


title: Sample20_598710: D00000000206103_DAY 1_Etanercept


title: Sample19_601778: D00000000206167_DAY 1_Etanercept


title: Sample9_599036: D00000000206452_WEEK 4_Tofacitinib


title: Sample6_606920: D00000000206500_WEEK 4_Tofacitinib


title: Sample8_600582: D00000000206422_DAY 1_Etanercept


title: Sample7_597886: D00000000206435_WEEK 4_Tofacitinib


title: Sample18_599042: D00000000206132_DAY 1_Tofacitinib


title: Sample16_600866: D00000000206132_WEEK 4_Tofacitinib


title: Sample4_609344: D00000000206456_WEEK 4_Tofacitinib


title: Sample5_610344: D00000000206468_DAY 1_Etanercept


title: Sample14_603686: D00000000206215_WEEK 4_Tofacitinib


title: Sample3_596320: D00000000206461_DAY 1_Tofacitinib


title: Sample15_588612: D00000000206316_DAY 1_Tofacitinib


title: Sample13_599154: D00000000206103_WEEK 4_Etanercept


title: Sample17_596410: D00000000206131_WEEK 4_Etanercept


title: Sample1_598682: D00000000206507_DAY 1_Etanercept


title: Sample2_609446: D00000000206447_WEEK 4_Etanercept


title: Sample93_599072: D00000000206156_DAY 1_Tofacitinib


title: Sample10_599144: D00000000206073_WEEK 4_Etanercept


title: Sample9_598370: D00000000206095_WEEK 4_Tofacitinib


title: Sample12_599192: D00000000206145_WEEK 4_Etanercept


title: Sample94_601630: D00000000206039_WEEK 4_Tofacitinib


title: Sample11_601498: D00000000206039_DAY 1_Tofacitinib


title: Amilo

city: Providence

first: David

middle: Thomas

last: Glidden

state: RI

address: 70 Ship St.

department: Molecular and Cell Biology

institute: Brown University

description:
PolyA+ RNA
Processed data files: rMATS_A3SS.txt, rMATS_A5SS.txt, rMATS_MXE.txt, rMATS_RI.txt, rMATS_SE.txt

data_processing:
Sequences were aligned to the hg19 reference genome using STAR version 2.5.1 with the following command-line parameters: --outSAMtype BAM SortedByCoordinate --limitBAMsortRAM 10000000000 --outSAMstrandField intronMotif --outSAMattrIHstart 0 --quantMode GeneCounts
Differential splicing analysis was done using rMATS version 3.2.5.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *.txt: Tab-delimited text files.

source_name: Human embryonic kidney cells

growth_protocol: Cells were grown in 10 cm plates using DMEM with 10% FBS and 1% penicillin/streptomycin.

extract_protocol:
Cells were lysed with TRIzol and RNA was extracted according to normal protocols.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Media was replaced with a fresh batch of media containing 300 µg/mL amiloride, and incubated for 6 h prior to RNA extraction.

tag: cell type

value: Embryonic kidney cells

value: Amiloride


title: Sample8_599198: D00000000206235_DAY 1_Etanercept


title: Sample92_585318: D00000000206064_WEEK 4_Tofacitinib


title: Sample5_594820: D00000000206157_DAY 1_Tofacitinib


title: Sample90_595806: D00000000206217_WEEK 4_Tofacitinib


title: Sample89_589518: D00000000206215_DAY 1_Tofacitinib


title: Sample91_602234: D00000000206109_DAY 1_Etanercept


title: Sample7_596422: D00000000206192_DAY 1_Tofacitinib


title: Ctrl


title: Sample4_585082: D00000000206221_WEEK 4_Etanercept


title: Sample87_599254: D00000000206046_WEEK 4_Tofacitinib


title: Sample88_602256: D00000000206274_DAY 1_Tofacitinib


title: Sample83_602624: D00000000206050_WEEK 4_Tofacitinib


title: Sample85_596696: D00000000206254_DAY 1_Etanercept


title: Sample82_596252: D00000000206131_DAY 1_Etanercept


title: Sample2_597820: D00000000206145_DAY 1_Etanercept


title: Sample6_610330: D00000000206097_WEEK 4_Tofacitinib


title: Sample81_598758: D00000000206113_DAY 1_Etanercept


title: Sample3_595700: D00000000206254_WEEK 4_Etanercept


title: Sample1_599180: D00000000206265_DAY 1_Etanercept


title: Sample80_602584: D00000000206147_WEEK 4_Etanercept


title: Sample77_597852: D00000000206121_DAY 1_Tofacitinib


title: Sample95_610376: D00000000205956_WEEK 4_Etanercept


title: Sample94_603646: D00000000205960_DAY 1_Etanercept


title: Sample78_610084: D00000000206284_WEEK 4_Etanercept


title: Sample76_599134: D00000000206113_WEEK 4_Etanercept


title: Sample93_600466: D00000000205985_WEEK 4_Tofacitinib


title: Sample75_597798: D00000000206033_DAY 1_Tofacitinib


title: Sample74_599066: D00000000206086_DAY 1_Tofacitinib


title: Sample73_602766: D00000000206095_DAY 1_Tofacitinib


title: Sample92_600916: D00000000205888_DAY 1_Etanercept


title: Sample79_599318: D00000000206221_DAY 1_Etanercept


title: Sample70_602598: D00000000206232_WEEK 4_Tofacitinib


title: Sample91_595560: D00000000206003_WEEK 4_Tofacitinib


title: Sample69_603060: D00000000206042_WEEK 4_Etanercept


title: Sample90_589963: D00000000205859_DAY 1_Tofacitinib


title: Sample68_598836: D00000000206147_DAY 1_Etanercept


title: Sample67_600512: D00000000206053_DAY 1_Tofacitinib


title: Sample66_602650: D00000000206232_DAY 1_Tofacitinib


title: Sample86_609576: D00000000206123_WEEK 4_Etanercept


title: Liver, day42, naïve, replicate 4

city: York

first: Paul

last: Kaye

address: Wentworth way

institute: University of York

hyb_protocol: Amplified RNA was then assayed using the SurePrint G3 mouse 8x60k microarray chip

scan_protocol: Samples were scanned using the agilent c surescan high resolution scanner

data_processing: Data was normalised using a 75th percentile shift method using GeneSpring software, version 9, agilent

source_name: Liver sample, day42 uninfected

label_protocol: standard agilent protocol

extract_protocol: RNA was isolated and amplified from tissue/blood using agilent low-input quick amp labelling kit.

treatment_protocol: 2x10^7 amastigotes were injected intravenously to propagate infection, 5 mice were untreated, and used for untreated spleen and liver samples at day36, 5 mice were untreated and used for spleen and tissue samples at day42 post infection.  5 mice were treated with ambisome,  and culled one day post ambisome treatment (day36), 5 mice were treated with ambisome and culled at day42, which was 8 days post treatment.

value: BALB/c

value: Liver

tag: status

value: naïve


title: Liver, day42, naïve, replicate 2


title: Liver, day36, infected ambisome treated replicate 5

source_name: Liver sample, day36 post infection, ambisome treated

value: infected

value: ambisome-treated


title: Sample89_596490: D00000000206006_DAY 1_Tofacitinib

value: DAY 1

value: Tofacitinib

tag: gender


title: Liver, day42, naïve, replicate 1


title: Liver, day42, naïve, replicate 3


title: Sample65_601254: D00000000206235_WEEK 4_Etanercept

value: WEEK 4


title: Liver, day36, infected ambisome treated replicate 2


title: Liver, day36, infected ambisome treated replicate 4


title: Liver, day36, infected ambisome treated replicate 3


title: Sample63_603008: D00000000206058_DAY 1_Tofacitinib


title: Sample88_601034: D00000000205961_DAY 1_Tofacitinib

value: NR


title: Liver, day36, naïve replicate 5

source_name: Liver sample, day36 uninfected


title: Sample71_600378: D00000000206241_DAY 1_Tofacitinib


title: Liver, day36, infected ambisome treated replicate 1


title: Sample64_585548: D00000000206265_WEEK 4_Etanercept

value: Etanercept 50 mg BIW

value: Etanercept


title: Sample62_609620: D00000000206123_DAY 1_Etanercept


title: Sample61_603206: D00000000206241_WEEK 4_Tofacitinib

value: R


title: Sample59_601006: D00000000206104_DAY 1_Etanercept


title: Sample58_610352: D00000000206097_DAY 1_Tofacitinib

value: F


title: Liver, day36, naïve replicate 4


title: Sample57_610114: D00000000206149_WEEK 4_Etanercept


title: Liver, day36, naïve replicate 3


title: Sample85_598850: D00000000205895_DAY 1_Tofacitinib


title: Sample56_603680: D00000000206073_DAY 1_Etanercept


title: Sample55_599324: D00000000206109_WEEK 4_Etanercept


title: Liver, day36, naïve replicate 2


title: Sample54_609420: D00000000206251_WEEK 4_Etanercept


title: Sample82_597788: D00000000205825_WEEK 4_Etanercept


title: Sample53_609450: D00000000206251_DAY 1_Etanercept


title: Sample83_601502: D00000000205828_WEEK 4_Etanercept


title: Sample81_601860: D00000000205945_WEEK 4_Etanercept


title: Sample87_597856: D00000000205861_DAY 1_Tofacitinib


title: Sample86_598382: D00000000205889_WEEK 4_Etanercept


title: Sample50_597858: D00000000206217_DAY 1_Tofacitinib


title: Sample51_600348: D00000000206100_DAY 1_Etanercept


title: Liver, day36, infected untreated replicate 5

source_name: Liver sample, day36 post infection, untreated

value: untreated


title: Liver, day36, naïve replicate 1


title: Sample49_599186: D00000000206121_WEEK 4_Tofacitinib

value: M


title: Sample46_602566: D00000000206192_WEEK 4_Tofacitinib


title: Sample47_596466: D00000000206286_DAY 1_Tofacitinib


title: Liver, day36, infected untreated replicate 4


title: Sample80_603056: D00000000205912_WEEK 4_Etanercept


title: Sample45_600874: D00000000206086_WEEK 4_Tofacitinib


title: Sample79_598426: D00000000205871_DAY 1_Tofacitinib


title: Sample95_596302: D00000000206286_WEEK 4_Tofacitinib


title: Sample78_606866: D00000000205973_DAY 1_Etanercept


title: Sample52_603018: D00000000206053_WEEK 4_Tofacitinib


title: Sample43_597854: D00000000206064_DAY 1_Tofacitinib


title: Sample44_609422: D00000000206266_DAY 1_Tofacitinib


title: Liver, day36, infected untreated replicate 2


title: Sample77_598956: D00000000206028_WEEK 4_Etanercept


title: Sample42_609394: D00000000206266_WEEK 4_Tofacitinib


title: Sample41_589636: D00000000206213_DAY 1_Etanercept


title: Sample76_609352: D00000000205976_WEEK 4_Tofacitinib


title: Sample38_597642: D00000000206104_WEEK 4_Etanercept


title: Liver, day36, infected untreated replicate 1


title: Sample40_598792: D00000000206050_DAY 1_Tofacitinib


title: Sample37_600846: D00000000206156_WEEK 4_Tofacitinib


title: Sample75_601694: D00000000206003_DAY 1_Tofacitinib


title: Sample39_602282: D00000000206274_WEEK 4_Tofacitinib


title: Sample74_597838: D00000000205841_DAY 1_Tofacitinib


title: Sample33_600384: D00000000206173_WEEK 4_Tofacitinib


title: Liver, day36, infected untreated replicate 3


title: Sample31_600482: D00000000206107_DAY 1_Tofacitinib


title: Sample71_609664: D00000000205831_WEEK 4_Tofacitinib


title: Sample30_597730: D00000000206058_WEEK 4_Tofacitinib


title: Sample28_603006: D00000000206100_WEEK 4_Etanercept


title: Sample29_600356: D00000000206042_DAY 1_Etanercept


title: Liver, day42, infected ambisome treated replicate 3

source_name: Liver sample, day42 post infection, ambisome treated


title: Liver, day42, infected ambisome treated replicate 2


title: Liver, day42, infected ambisome treated replicate 5


title: Sample70_602510: D00000000206006_WEEK 4_Tofacitinib


title: Liver, day42, infected ambisome treated replicate 4


title: Liver, day42, infected untreated replicate 4

source_name: Liver sample, day42 post infection, untreated


title: Liver, day42, infected untreated replicate 5


title: Liver, day42, infected ambisome treated replicate 1


title: Sample27_601988: D00000000206316_WEEK 4_Tofacitinib


title: Sample35_585618: D00000000205981_DAY 1_Tofacitinib


title: Sample32_599300: D00000000206033_WEEK 4_Tofacitinib


title: Sample69_606916: D00000000205952_DAY 1_Tofacitinib


title: Sample68_607154: D00000000205973_WEEK 4_Etanercept


title: Sample34_610018: D00000000206284_DAY 1_Etanercept


title: Sample67_602128: D00000000205825_DAY 1_Etanercept


title: Sample25_610136: D00000000206149_DAY 1_Etanercept


title: Sample26_595462: D00000000206167_WEEK 4_Etanercept


title: Sample23_603046: D00000000206107_WEEK 4_Tofacitinib


title: Sample22_602056: D00000000206157_WEEK 4_Tofacitinib


title: Sample21_602124: D00000000206173_DAY 1_Tofacitinib


title: Sample66_599296: D00000000206001_WEEK 4_Etanercept


title: Sample24_597890: D00000000206046_DAY 1_Tofacitinib


title: Sample20_598710: D00000000206103_DAY 1_Etanercept


title: Sample65_594818: D00000000205871_WEEK 4_Tofacitinib


title: Sample18_599042: D00000000206132_DAY 1_Tofacitinib


title: Sample17_596410: D00000000206131_WEEK 4_Etanercept


title: Sample16_600866: D00000000206132_WEEK 4_Tofacitinib


title: Sample15_588612: D00000000206316_DAY 1_Tofacitinib


title: Sample63_601168: D00000000205970_DAY 1_Tofacitinib


title: Sample13_599154: D00000000206103_WEEK 4_Etanercept


title: Sample62_602664: D00000000205920_DAY 1_Etanercept


title: Spleen, day42 infected untreated replicate 4

source_name: Spleen sample, day42 post infection, untreated

value: Spleen


title: Liver, day42, infected untreated replicate 1


title: Liver, day42, infected untreated replicate 2


title: Spleen, day42 infected untreated replicate 5


title: Liver, day42, infected untreated replicate 3


title: Sample61_598912: D00000000205994_DAY 1_Etanercept


title: Sample11_601498: D00000000206039_DAY 1_Tofacitinib


title: Sample10_599144: D00000000206073_WEEK 4_Etanercept


title: Spleen day42 naïve, replicate 5

source_name: Spleen sample, day42 uninfected


title: Sample9_598370: D00000000206095_WEEK 4_Tofacitinib


title: Sample8_599198: D00000000206235_DAY 1_Etanercept


title: Sample7_596422: D00000000206192_DAY 1_Tofacitinib


title: Sample6_610330: D00000000206097_WEEK 4_Tofacitinib


title: Sample64_607200: D00000000205952_WEEK 4_Tofacitinib


title: Sample12_599192: D00000000206145_WEEK 4_Etanercept


title: Sample14_603686: D00000000206215_WEEK 4_Tofacitinib


title: Spleen, day42 infected untreated replicate 3


title: Sample73_606954: D00000000205919_DAY 1_Tofacitinib


title: Sample4_585082: D00000000206221_WEEK 4_Etanercept


title: Spleen day42 naïve, replicate 4


title: Sample3_595700: D00000000206254_WEEK 4_Etanercept


title: Sample57_607234: D00000000205940_WEEK 4_Tofacitinib


title: Sample2_597820: D00000000206145_DAY 1_Etanercept


title: Sample59_595716: D00000000206020_DAY 1_Etanercept


title: Sample1_599180: D00000000206265_DAY 1_Etanercept


title: Sample56_601644: D00000000205970_WEEK 4_Tofacitinib


title: Sample55_595748: D00000000206028_DAY 1_Etanercept


title: Sample54_598702: D00000000205877_DAY 1_Etanercept


title: Sample58_599084: D00000000205994_WEEK 4_Etanercept


title: Sample94_603646: D00000000205960_DAY 1_Etanercept


title: Sample95_610376: D00000000205956_WEEK 4_Etanercept


title: Sample5_594820: D00000000206157_DAY 1_Tofacitinib


title: Spleen day42 naïve, replicate 1


title: Spleen, day42 infected, ambisome treated replicate 5

source_name: Spleen sample, day42 post infection, ambisome treated


title: Spleen, day42 infected untreated replicate 1


title: Spleen day42 naïve, replicate 3


title: Sample92_600916: D00000000205888_DAY 1_Etanercept


title: Sample53_601148: D00000000205938_WEEK 4_Tofacitinib


title: Sample91_595560: D00000000206003_WEEK 4_Tofacitinib


title: Spleen, day42 infected, ambisome treated replicate 3


title: Sample90_589963: D00000000205859_DAY 1_Tofacitinib


title: Spleen day42 naïve, replicate 2


title: Sample89_596490: D00000000206006_DAY 1_Tofacitinib


title: Sample93_600466: D00000000205985_WEEK 4_Tofacitinib


title: Sample86_598382: D00000000205889_WEEK 4_Etanercept


title: Spleen, day42 infected, ambisome treated replicate 1


title: Sample50_588642: D00000000206007_DAY 1_Etanercept


title: Sample83_601502: D00000000205828_WEEK 4_Etanercept


title: Sample82_597788: D00000000205825_WEEK 4_Etanercept


title: Sample87_597856: D00000000205861_DAY 1_Tofacitinib


title: Spleen, day36 infected, untreated replicate 5

source_name: Spleen sample, day36 post infection, untreated


title: Sample49_594812: D00000000205834_WEEK 4_Etanercept


title: Spleen, day42 infected, ambisome treated replicate 2


title: Spleen, day36 infected, untreated replicate 3


title: Sample52_598686: D00000000205855_DAY 1_Tofacitinib


title: Sample47_598506: D00000000205998_WEEK 4_Etanercept


title: Sample80_603056: D00000000205912_WEEK 4_Etanercept


title: Sample79_598426: D00000000205871_DAY 1_Tofacitinib


title: Sample45_597422: D00000000205888_WEEK 4_Etanercept


title: Sample77_598956: D00000000206028_WEEK 4_Etanercept


title: Sample44_584792: D00000000205938_DAY 1_Tofacitinib


title: Sample75_601694: D00000000206003_DAY 1_Tofacitinib


title: Sample73_606954: D00000000205919_DAY 1_Tofacitinib


title: Sample71_609664: D00000000205831_WEEK 4_Tofacitinib


title: Sample70_602510: D00000000206006_WEEK 4_Tofacitinib


title: Sample81_601860: D00000000205945_WEEK 4_Etanercept


title: Spleen, day36 infected, untreated replicate 4


title: Spleen, day36 infected, untreated replicate 2


title: Spleen, day36 infected, untreated replicate 1


title: Spleen, day36 naïve, replicate 5

source_name: Spleen sample, day36 uninfected


title: Sample43_599038: D00000000205855_WEEK 4_Tofacitinib


title: Sample68_607154: D00000000205973_WEEK 4_Etanercept


title: Sample46_597392: D00000000205862_DAY 1_Tofacitinib


title: Sample42_603086: D00000000205995_DAY 1_Tofacitinib


title: Spleen, day36 naïve, replicate 3


title: Sample67_602128: D00000000205825_DAY 1_Etanercept


title: Sample76_609352: D00000000205976_WEEK 4_Tofacitinib


title: Spleen, day36 naïve, replicate 2


title: Sample64_607200: D00000000205952_WEEK 4_Tofacitinib


title: Sample41_600366: D00000000205913_WEEK 4_Etanercept


title: Sample65_594818: D00000000205871_WEEK 4_Tofacitinib


title: Sample40_602602: D00000000205828_DAY 1_Etanercept


title: Sample69_606916: D00000000205952_DAY 1_Tofacitinib


title: Sample63_601168: D00000000205970_DAY 1_Tofacitinib


title: Spleen, day36 naïve, replicate 1


title: Sample62_602664: D00000000205920_DAY 1_Etanercept


title: Sample78_606866: D00000000205973_DAY 1_Etanercept


title: Sample61_598912: D00000000205994_DAY 1_Etanercept


title: Sample57_607234: D00000000205940_WEEK 4_Tofacitinib


title: Sample58_599084: D00000000205994_WEEK 4_Etanercept


title: Sample59_595716: D00000000206020_DAY 1_Etanercept


title: Sample38_603684: D00000000205859_WEEK 4_Tofacitinib


title: Sample35_601226: D00000000205839_DAY 1_Tofacitinib


title: Spleen, day36 infected, ambisome treated replicate 4

source_name: Spleen sample, day36 post infection, ambisome treated


title: Sample32_597416: D00000000205995_WEEK 4_Tofacitinib


title: Spleen, day36 infected, ambisome treated replicate 3


title: Sample53_601148: D00000000205938_WEEK 4_Tofacitinib


title: Sample55_595748: D00000000206028_DAY 1_Etanercept


title: Sample56_601644: D00000000205970_WEEK 4_Tofacitinib


title: Spleen, day36 infected, ambisome treated replicate 5


title: Spleen, day36 infected, ambisome treated replicate 1


title: Spleen, day36 infected, ambisome treated replicate 2


title: Sample54_598702: D00000000205877_DAY 1_Etanercept


title: Sample51_597362: D00000000205815_DAY 1_Tofacitinib

source_name: Blood_DAY 1_Tofacitinib


title: Sample50_588642: D00000000206007_DAY 1_Etanercept


title: Sample30_589546: D00000000205834_DAY 1_Etanercept


title: Sample46_597392: D00000000205862_DAY 1_Tofacitinib


title: Sample66_599296: D00000000206001_WEEK 4_Etanercept

source_name: Blood_WEEK 4_Etanercept


title: Sample29_597570: D00000000205913_DAY 1_Etanercept


title: Sample45_597422: D00000000205888_WEEK 4_Etanercept


title: Sample39_585618: D00000000205981_DAY 1_Tofacitinib


title: Sample33_602642: D00000000205998_DAY 1_Etanercept


title: Sample42_603086: D00000000205995_DAY 1_Tofacitinib


title: Sample28_607360: D00000000205904_WEEK 4_Etanercept


title: Sample43_599038: D00000000205855_WEEK 4_Tofacitinib

source_name: Blood_WEEK 4_Tofacitinib


title: ko_testes_1

value: testes

tag: lncrna previous name

tag: background

value: C57BL/6J (N3-C57BL/6J, no Neo)

tag: official strain name

tag: genotype

value: ko

tag: Sex


title: Sample27_595648: D00000000205815_WEEK 4_Tofacitinib

tag: visit

tag: treatmentshort

tag: pasi

tag: tag

tag: age


title: Sample31_600504: D00000000205912_DAY 1_Etanercept

source_name: Blood_DAY 1_Etanercept

tag: treatment

tag: platesimple

tag: plate


title: Sample52_598686: D00000000205855_DAY 1_Tofacitinib


title: Sample44_584792: D00000000205938_DAY 1_Tofacitinib


title: Sample37_602012: D00000000206007_WEEK 4_Etanercept


title: Sample38_603684: D00000000205859_WEEK 4_Tofacitinib


title: Sample47_598506: D00000000205998_WEEK 4_Etanercept


title: Sample49_594812: D00000000205834_WEEK 4_Etanercept


title: ko_testes_2

tag: tissue


title: ko_testes_0


title: Sample35_601226: D00000000205839_DAY 1_Tofacitinib


title: Sample25_610406: D00000000205956_DAY 1_Etanercept


title: Spleen, day36 naïve, replicate 4

tag: strain

value: BALB/c

tag: time

value: naïve


title: Sample34_609340: D00000000205831_DAY 1_Tofacitinib

tag: gender


title: Sample41_600366: D00000000205913_WEEK 4_Etanercept


title: wt_testes_2

tag: lncrna previous name

value: wt


title: Sample24_602600: D00000000205889_DAY 1_Etanercept

value: DAY 1


title: Sample33_602642: D00000000205998_DAY 1_Etanercept


title: wt_testes_3

tag: background


title: Sample22_597822: D00000000206001_DAY 1_Etanercept


title: Sample26_599316: D00000000205861_WEEK 4_Tofacitinib

value: Tofacitinib


title: Sample30_589546: D00000000205834_DAY 1_Etanercept


title: Sample40_602602: D00000000205828_DAY 1_Etanercept


title: Sample32_597416: D00000000205995_WEEK 4_Tofacitinib

value: WEEK 4


title: wt_testes_0

tag: official strain name


title: wt_prostate_2

value: prostate

tag: genotype


title: wt_testes_1

tag: Sex


title: Sample29_597570: D00000000205913_DAY 1_Etanercept

tag: visit

value: Etanercept 50 mg BIW


title: Sample28_607360: D00000000205904_WEEK 4_Etanercept

tag: treatmentshort

value: Etanercept


title: Sample27_595648: D00000000205815_WEEK 4_Tofacitinib

tag: pasi

value: NR


title: Sample21_588814: D00000000205962_DAY 1_Tofacitinib

tag: tag

value: R


tag: age


title: Sample20_597784: D00000000205862_WEEK 4_Tofacitinib

tag: treatment


title: Sample18_607420: D00000000205904_DAY 1_Etanercept

tag: platesimple


title: Sample19_597882: D00000000205961_WEEK 4_Tofacitinib

tag: plate


title: Sample23_598974: D00000000206020_WEEK 4_Etanercept

value: F


title: wt_prostate_0

tag: tissue

value: M


title: ko_prostate_1


title: Sample17_598408: D00000000205960_WEEK 4_Etanercept


title: wt_prostate_1


title: Sample16_601336: D00000000205981_WEEK 4_Tofacitinib


title: wt_eye_0

value: eye


title: wt_eye_2


title: Sample15_602312: D00000000205985_DAY 1_Tofacitinib


title: Sample14_609924: D00000000206030_WEEK 4_Etanercept


title: Sample13_599092: D00000000205895_WEEK 4_Tofacitinib


title: Sample12_607192: D00000000205940_DAY 1_Tofacitinib


title: Sample11_598500: D00000000205945_DAY 1_Etanercept


title: wt_eye_1


title: Sample26_599316: D00000000205861_WEEK 4_Tofacitinib


title: Sample10_603658: D00000000205962_WEEK 4_Tofacitinib


title: ko_eye_0


title: ko_eye_1


title: Sample8_603668: D00000000205963_DAY 1_Tofacitinib


title: Sample7_598998: D00000000205963_WEEK 4_Tofacitinib


title: Sample6_609370: D00000000205976_DAY 1_Tofacitinib


title: ko_eye_2


title: Sample5_599096: D00000000205877_WEEK 4_Etanercept


title: ko_prostate_0


title: wt_spleen_0

value: spleen


title: Sample4_610368: D00000000206030_DAY 1_Etanercept


title: Sample9_585122: D00000000205841_WEEK 4_Tofacitinib


title: wt_spleen_2

value: C57BL/6J (N3-C57BL/6J, no Neo)


title: Sample2_606962: D00000000205919_WEEK 4_Tofacitinib


title: Sample3_602760: D00000000205920_WEEK 4_Etanercept


title: ko_spleen_1

value: ko


title: Sample93_599076: D00000000205786_WEEK 4_Tofacitinib


title: Sample1_598450: D00000000205839_WEEK 4_Tofacitinib


title: Sample91_609986: D00000000205615_WEEK 4_Tofacitinib


title: Sample92_599328: D00000000205732_WEEK 4_Tofacitinib


title: Sample90_595752: D00000000205712_DAY 1_Tofacitinib


title: ko_spleen_0


title: LGSCs_P20

first: Yan

state: Guangdong

address: No.132, East Outer Ring Road，Guangzhou Higher Education Mega Center

department: School of Life Sciences

institute: Sun Yat-sen University

data_processing:
Illumina Casava 1.8 software was used for basecalls.
Paired-end clean reads were aligned to the reference genome using Hisat2(v2.0.5)
FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, was calculated based on the length of each gene and reads count mapped to this gene (Trapnell, Cole, et al., 2010).
Genome_build: NCBIM37
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: Lacrimal gland stem cells

growth_protocol: For LGSCs primary culture, 6-8 week-old mice were sacrificed. Then the LGs were cut into small fragments (about 1 mm3), treated with 25 U/ml Dispase (BD Biosciences) and 0.1% Collagenase Ⅰ (Gibco) for 1 hour at 37℃, and treated with 0.05% trypsin (Sigma) for 10 min at 37℃ to dissociate into single cells by pipetting. 1×104 cells were seeded into 80 μl Matrigel-LGSCM matrix (Matrigel: LGSCM= 1:1) per well of 24-well plate. The well was pre-coated with 20 μl Matrigel-LGSCM matrix. After incubation for 20 min at 37℃, the mix was solidified, then 600 μl LGSCM was added, which contained DMEM/F12 (1:1 mixture of Dulbecco’s Modified Eagle’s Medium and Ham’s F-12) (Sigma), N2 (Gibco), B27 (Gibco), L-glutaMAX (Gibco), NEAA ( Non-Essential Amino Acids, Gibco), murine EGF (PeproTech), FGF10 (PeproTech), Wnt3A (PeproTech) and Y-27632 (Selleck). For LGSCs passage, LGSCs-spheres cultured for 7 days were released by incubating in 10 U/ml Dispase for 1 hour at 37℃, then treated with 0.05% trypsin for 5 min at 37℃ to dissociate single cells, and planted the single cells like the protocol in primary culture.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen), and mRNA was purified from total RNA using poly-T oligo-attached magnetic beads.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

tag: strain

tag: cell type

value: Lacrimal gland stem cells

tag: culture time

value: 7 days

tag: cell passage number


title: Sample89_603166: D00000000205621_DAY 1_Etanercept

tag: gender


title: Sample87_601638: D00000000205575_DAY 1_Etanercept


title: wt_spleen_1

tag: lncrna previous name

tag: background

tag: official strain name

value: wt


title: Sample88_606872: D00000000205607_WEEK 4_Tofacitinib

tag: visit


tag: treatmentshort


value: DAY 1

tag: pasi


title: ko_liver_2

value: liver

tag: genotype

tag: Sex


title: Sample86_607486: D00000000205585_WEEK 4_Etanercept

value: WEEK 4

tag: treatment

tag: tag

tag: age


title: ko_spleen_2

tag: tissue


tag: platesimple

tag: plate


title: LGSCs_P10

tag: strain

tag: cell type

tag: culture time


title: Sample85_602308: D00000000205796_DAY 1_Etanercept

tag: gender


title: ko_liver_1

tag: lncrna previous name

tag: background


title: LGSCs_P6

tag: cell passage number


title: wt_liver_2

tag: official strain name


title: Sample83_601376: D00000000205715_WEEK 4_Tofacitinib

tag: visit

tag: treatmentshort

value: Tofacitinib

tag: pasi


title: Sample84_603656: D00000000205719_WEEK 4_Tofacitinib

tag: treatment


tag: tag


title: ko_liver_0

tag: genotype

tag: Sex


title: Sample95_599076: D00000000205786_WEEK 4_Tofacitinib

tag: age

tag: platesimple


title: 10870rocAFIXED (2)

city: Reno

last: Sumby

state: NV

address: 1554 N. Virginia St.

department: Microbiology & Immunology

institute: University of Nevada

data_processing:
CLC Genomics Workbench version 7.5.1 RNA-seq was used for basecalling and aligning the sequence reads to the MGAS315 genome
Parameters for alignment were set up:  Similar fraction=0.8, Length fraction=0.8, Mismatch cost=2, Insertion cost=3.
Normalization was performed to overall sequencing depth using total mapped reads data.
Statistical significance was tested using Kal’s Z-test with a false-discovery rate correction.
Genome_build: ASM742v1
Supplementary_files_format_and_content: File containing columns for the gene name, Kal's Z-test with FDR correction value, normalized mean for each strain, gene start nucleotide number, gene stop nucleotide number, and expression ratios

organism: Streptococcus pyogenes

source_name: 10870rocAFIXED (2)

growth_protocol: GAS strains were grown in THY broth to the stationary phase of growth (four hours after reaching an O.D.600 of 0.5)

extract_protocol:
Total RNA was isolated and rRNAs were depleted using the Ribo-Zero Gram-Positive rRNA Removal Kit (Epicentre).
The rRNA depleted RNA was used to generate cDNA libraries using the ScriptSeq kit (Epicentre).  Briefly, RNA was fragmented, cDNA was synthesized using random hexamers containing a 5′ tagging sequence, the RNA was hydrolyzed, and the cDNA was tagged at the 3′ end.  A limited number of PCR cycles (n=12) were used to amplify the libraries via the 5′ and 3′ tags (the libraries were barcoded by using different primers), and the libraries size-selected (170 to 300 bp).  The size-selected and barcoded libraries were run on an Illumina HiSeq flowcell.

tag: isolate

value: Derivative of MGAS10870 with a functional rocA allele (10870rocAFIXED)

tag: growth stage

value: Stationary phase of growth

tag: growth medium

value: THY broth growth


title: 10870rocAFIXED (1)

source_name: 10870rocAFIXED (1)


title: Sample94_599328: D00000000205732_WEEK 4_Tofacitinib

value: R

tag: gender

tag: plate


title: MGAS10870 (2)

value: Parental M3 GAS isolate (MGAS10870)


title: wt_liver_1

tag: tissue

tag: lncrna previous name

tag: background

value: M


title: Sample81_601296: D00000000205763_WEEK 4_Tofacitinib

tag: visit


title: Sample93_609986: D00000000205615_WEEK 4_Tofacitinib

tag: treatmentshort

value: NR

value: F


title: MGAS10870 (1)


title: Sample80_598868: D00000000205801_DAY 1_Tofacitinib

tag: pasi


title: Sample92_595752: D00000000205712_DAY 1_Tofacitinib

tag: treatment


title: wt_liver_0

value: C57BL/6J (N3-C57BL/6J, no Neo)

tag: official strain name


title: M1ΔrocA (2)

data_processing:
CLC Genomics Workbench version 7.5.1 RNA-seq was used for basecalling and aligning the sequence reads to the MGAS5005 genome
Parameters for alignment were set up:  Similar fraction=0.8, Length fraction=0.8, Mismatch cost=2, Insertion cost=3.
Normalization was performed to overall sequencing depth using total mapped reads data.
Statistical significance was tested using Kal’s Z-test with a false-discovery rate correction.
Genome_build: ASM1176v2
Supplementary_files_format_and_content: File containing columns for the gene name, Kal's Z-test with FDR correction value, normalized mean for each strain, gene start nucleotide number, gene stop nucleotide number, and expression ratios

source_name: M1ΔrocA (2)

value: Derivative of MGAS2221 that lacks rocA (M1<delta>rocA)


title: wt_heart_0

value: heart

tag: genotype


title: wt_heart_2

tag: Sex


title: MGAS2221 (2)

value: Parental M1 GAS isolate (MGAS2221)


title: Sample91_603166: D00000000205621_DAY 1_Etanercept

value: Etanercept 50 mg BIW

value: Etanercept

tag: tag

tag: age


title: Sample90_606872: D00000000205607_WEEK 4_Tofacitinib

tag: platesimple


title: Sample78_599034: D00000000205693_WEEK 4_Etanercept


title: Sample77_602048: D00000000205645_WEEK 4_Tofacitinib


title: Sample79_599258: D00000000205726_WEEK 4_Etanercept


title: M1ΔrocA (1)

source_name: M1ΔrocA (1)

tag: isolate

tag: growth stage


title: ko_heart_2

value: ko


title: MGAS2221 (1)

tag: growth medium


title: ko_heart_1


title: Sample87_602308: D00000000205796_DAY 1_Etanercept

value: DAY 1

tag: gender

tag: plate


title: Sample89_601638: D00000000205575_DAY 1_Etanercept


title: Sample88_607486: D00000000205585_WEEK 4_Etanercept

value: WEEK 4